Human Volunteer Study - Differential Abundance Testing
Scott A. Handley and Barry Hykes Jr.
October 27, 2017
Load phyloseq data generated from dada2
# Load Phyloseq object generated in HIV_oral_preprocessing.Rmd
# Options include GreenGenes, SILVA, RDP and HitDB
ps1 <- readRDS("~/Dropbox/Research/human_volunteer/results/ps1.RDS")
ps1## phyloseq-class experiment-level object
## otu_table() OTU Table: [ 1590 taxa and 100 samples ]
## sample_data() Sample Data: [ 100 samples by 119 sample variables ]
## tax_table() Taxonomy Table: [ 1590 taxa by 7 taxonomic ranks ]
## phy_tree() Phylogenetic Tree: [ 1590 tips and 1588 internal nodes ]# View sample variables & generate basic stats
sample_variables(ps1)## [1] "X.SampleID" "BarcodeSequence"
## [3] "LinkerPrimerSequence" "sequence_ID"
## [5] "miseq_run" "plate"
## [7] "well" "collaborator"
## [9] "tissue" "number_seqs_slout"
## [11] "sample_surviving_dada2" "sample_ID"
## [13] "tube_ID" "patient_ID"
## [15] "randomization" "day"
## [17] "randomization_arm" "Date_assessment"
## [19] "Age" "Gender"
## [21] "Ethnicity" "Asthma"
## [23] "Eczema" "Hayfever"
## [25] "Allergies" "Def_allergies"
## [27] "Other_illness" "Chronic_medication"
## [29] "Def_medication" "Herbs_OTC"
## [31] "def_Herbs_OTC" "Alcohol"
## [33] "Alcoholunitsweek" "Smoking"
## [35] "Drugs" "Drugstype"
## [37] "Drugsusage" "Weight"
## [39] "Length" "BMIcalc"
## [41] "SystolicBP" "DiastolicBP"
## [43] "Pulse" "Respfreq"
## [45] "Physical_exam_abnorm" "def_phys_abnormalities"
## [47] "Lab_abnorm_screen" "def_abnorm_lab_screen"
## [49] "Serum_screen" "PBMC_screen"
## [51] "Feces_screen" "Date_day_9"
## [53] "New_medication_day_9" "def_new_med_day_9"
## [55] "Course_completed" "Antibiotic_side_effects"
## [57] "Def_abx_side_effects" "Lab_abnorm_post_antibiotics"
## [59] "def_abnorm_post_antibiotics" "Date_day_0"
## [61] "Feces_day_0" "New_medication_day0"
## [63] "Def_new_medication_day_0" "Vaccination_side_effects"
## [65] "Def_vac_side_effects" "Lab_abnorm_post_vaccination"
## [67] "def_abnorm_post_vaccination" "Date_day_7"
## [69] "Feces_day_1" "Feces_day_2"
## [71] "Feces_day_3" "Feces_day_4"
## [73] "Feces_day_5" "Feces_day_6"
## [75] "Feces_day_7" "Serum_day_7"
## [77] "New_medication_day7" "def_new_med_day7"
## [79] "Date_day_14" "New_medication_day14"
## [81] "def_new_med_day14" "Serum_day_14"
## [83] "PBMC_day_14" "Date_day_28"
## [85] "New_medication_day28" "def_new_med_day28"
## [87] "Serum_day_28" "PBMC_day_28"
## [89] "Study_complete" "pre_RV_IgA"
## [91] "d7_RV_IgA" "boost_change"
## [93] "d7_RV_IgA_boost_fc" "d7_roto_boost"
## [95] "d7_rota_boost_updated" "d14_RV_IgA"
## [97] "d28_RV_IgA" "RV_Ag_shedding_d0"
## [99] "RV_Ag_shedding_d1" "RV_Ag_shedding_d2"
## [101] "RV_Ag_shedding_d3" "RV_Ag_shedding_d4"
## [103] "RV_Ag_shedding_d5" "RV_Ag_shedding_d6"
## [105] "Shedding" "pneumo_IgG_pre"
## [107] "pneumo_IgG_7" "pneumo_IgG_14"
## [109] "pneumo_IgG_28" "pneumo_IgG_7vPre"
## [111] "pneumo_IgG_14vPre" "pneumo_IgG_28vPre"
## [113] "tetanus_IgG_pre" "tetanus_IgG_d7"
## [115] "tetanus_IgG_d14" "tetanus_IgG_d28"
## [117] "tetanus_IgG_7vPre" "tetanus_IgG_14vPre"
## [119] "tetanus_IgG_28vPre"sd(sample_sums(ps1))## [1] 22713.02get_taxa_unique(ps1, "Phylum")## [1] "Bacteroidetes" "Firmicutes" "Verrucomicrobia"
## [4] "Proteobacteria" "Fusobacteria" "Synergistetes"
## [7] "Actinobacteria" "Spirochaetes" "Lentisphaerae"
## [10] "Euryarchaeota" "Elusimicrobia" "Tenericutes"Differential abundance testing
Likelihood ratio test: Identifying taxa differentially abundant in one or more time points between 1) patients who boosted versus thoses that did not and 2) patients that shed rotavirus in their stool and those that did not
1) Rotavirus Boost or Not
Only testing for categories where there were > 2 samples per variable (boost or Shedding)
BOOST: NARROW SPECTRUM ANTIBIOTICS SAMPLES
# Test for taxa which at one or more time points after time 0 showed a d7-rota-boost-specific effect
# Convert phyloseq object to DeSeq2 table
ds.boost.narrow.LRT <- phyloseq_to_deseq2(ps1.narrow, ~d7_rota_boost_updated + day + d7_rota_boost_updated:day)
# Calculate geometric means prior to estimate size factors
geoMeans.ds.boost.narrow.LRT <- apply(counts(ds.boost.narrow.LRT), 1, gm_mean)
ds.boost.narrow.LRT <- estimateSizeFactors(ds.boost.narrow.LRT, geoMeans = geoMeans.ds.boost.narrow.LRT)
# Run DeSeq2
dds.boost.narrow.LRT <- DESeq(ds.boost.narrow.LRT, test="LRT", reduced = ~d7_rota_boost_updated + day)
# Tabulate results
res.dds.boost.narrow.LRT = results(dds.boost.narrow.LRT)
res.dds.boost.narrow.LRT$symbol <- mcols(dds.boost.narrow.LRT)$symbol
head(res.dds.boost.narrow.LRT[order(res.dds.boost.narrow.LRT$padj), ], 4)## log2 fold change (MLE): d7 rota boost updatedYes.day7
## LRT p-value: '~ d7_rota_boost_updated + day + d7_rota_boost_updated:day' vs '~ d7_rota_boost_updated + day'
## DataFrame with 4 rows and 6 columns
## baseMean
## <numeric>
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 5327.853
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 1017.600
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 842.095
## TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG 1923.573
## log2FoldChange
## <numeric>
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 3.6496383
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 0.6975514
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT -0.8585548
## TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG -2.0919430
## lfcSE
## <numeric>
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 6.128345
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 5.265614
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 4.588674
## TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG 5.687215
## stat
## <numeric>
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 0.35086417
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 0.96287868
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 0.03470478
## TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG 0.15368236
## pvalue
## <numeric>
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 0.8390944
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 0.6178934
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 0.9827973
## TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG 0.9260369
## padj
## <numeric>
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 1
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 1
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 1
## TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG 1write.table(res.dds.boost.narrow.LRT, file = "./results/deseq_rotaboost_narrow_LRT.txt", sep = "\t")
mcols(res.dds.boost.narrow.LRT)## DataFrame with 6 rows and 2 columns
## type
## <character>
## 1 intermediate
## 2 results
## 3 results
## 4 results
## 5 results
## 6 results
## description
## <character>
## 1 mean of normalized counts for all samples
## 2 log2 fold change (MLE): d7 rota boost updatedYes.day7
## 3 standard error: d7 rota boost updatedYes.day7
## 4 LRT statistic: '~ d7_rota_boost_updated + day + d7_rota_boost_updated:day' vs '~ d7_rota_boost_updated + day'
## 5 LRT p-value: '~ d7_rota_boost_updated + day + d7_rota_boost_updated:day' vs '~ d7_rota_boost_updated + day'
## 6 BH adjusted p-valuessummary(res.dds.boost.narrow.LRT)##
## out of 830 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up) : 0, 0%
## LFC < 0 (down) : 0, 0%
## outliers [1] : 268, 32%
## low counts [2] : 133, 16%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results# Plot taxa with lowest p-value
fiss.dds.boost.narrow.LRT <- plotCounts(dds.boost.narrow.LRT, which.min(res.dds.boost.narrow.LRT$padj),
intgroup = c("day","d7_rota_boost_updated"), returnData = TRUE)
ggplot(fiss.dds.boost.narrow.LRT,
aes(x = as.numeric(day), y = count, color = d7_rota_boost_updated, group = d7_rota_boost_updated)) +
geom_point() + geom_smooth(se = FALSE, method = "loess") + scale_y_log10()
Interpretation: There are no differentially abundant taxa in any of the randomization arms at any time point between samples that boosted and those that did not boost in narrow spectrum antibiotics treated samples.
2) Shedding or Not: Control samples not analyzed as two few shedders in that group.
Shedding: NARROW SPECTRUM ANTIBIOTICS SAMPLES
# Test for taxa which at one or more time points after time 0 showed a Shedding-specific effect
# Convert phyloseq object to DeSeq2 table
ds.Shedding.narrow.LRT <- phyloseq_to_deseq2(ps1.narrow, ~Shedding + day + Shedding:day)
# Calculate geometric means prior to estimate size factors
geoMeans.ds.Shedding.narrow.LRT <- apply(counts(ds.Shedding.narrow.LRT), 1, gm_mean)
ds.Shedding.narrow.LRT <- estimateSizeFactors(ds.Shedding.narrow.LRT, geoMeans = geoMeans.ds.Shedding.narrow.LRT)
# Run DeSeq2
dds.Shedding.narrow.LRT <- DESeq(ds.Shedding.narrow.LRT, test="LRT", reduced = ~Shedding + day)
# Tabulate results
res.dds.Shedding.narrow.LRT = results(dds.Shedding.narrow.LRT)
res.dds.Shedding.narrow.LRT$symbol <- mcols(dds.Shedding.narrow.LRT)$symbol
head(res.dds.Shedding.narrow.LRT[order(res.dds.Shedding.narrow.LRT$padj), ], 4)## log2 fold change (MLE): SheddingShedding.day7
## LRT p-value: '~ Shedding + day + Shedding:day' vs '~ Shedding + day'
## DataFrame with 4 rows and 6 columns
## baseMean
## <numeric>
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 5327.853
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 1017.600
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 842.095
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 1642.889
## log2FoldChange
## <numeric>
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT -0.9416984
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT -3.2646342
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT -2.0524161
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT -30.0000000
## lfcSE
## <numeric>
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 6.204814
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 5.451830
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 4.732296
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 7.953654
## stat
## <numeric>
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 3.2560877
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 0.6442059
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 0.1880057
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 3.1519792
## pvalue
## <numeric>
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 0.1963132
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 0.7246236
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 0.9102802
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 0.2068028
## padj
## <numeric>
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 1
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 1
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 1
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 1write.table(res.dds.Shedding.narrow.LRT, file = "./results/deseq_Shedding_narrow_LRT.txt", sep = "\t")
mcols(res.dds.Shedding.narrow.LRT)## DataFrame with 6 rows and 2 columns
## type
## <character>
## 1 intermediate
## 2 results
## 3 results
## 4 results
## 5 results
## 6 results
## description
## <character>
## 1 mean of normalized counts for all samples
## 2 log2 fold change (MLE): SheddingShedding.day7
## 3 standard error: SheddingShedding.day7
## 4 LRT statistic: '~ Shedding + day + Shedding:day' vs '~ Shedding + day'
## 5 LRT p-value: '~ Shedding + day + Shedding:day' vs '~ Shedding + day'
## 6 BH adjusted p-valuessummary(res.dds.Shedding.narrow.LRT)##
## out of 839 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up) : 0, 0%
## LFC < 0 (down) : 0, 0%
## outliers [1] : 264, 31%
## low counts [2] : 124, 15%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results# Plot taxa with lowest p-value
fiss.dds.Shedding.narrow.LRT <- plotCounts(dds.Shedding.narrow.LRT, which.min(res.dds.Shedding.narrow.LRT$padj),
intgroup = c("day","d7_rota_boost_updated"), returnData = TRUE)
ggplot(fiss.dds.Shedding.narrow.LRT,
aes(x = as.numeric(day), y = count, color = d7_rota_boost_updated, group = d7_rota_boost_updated)) +
geom_point() + geom_smooth(se = FALSE, method = "loess") + scale_y_log10()
Interpretation: There are no differentially abundant taxa in any of the randomization arms at any time point between samples that shed rotavirus and those that did not.
Pairwise differential abundance testing
BOOST: Day -9 Narrow Spectrum Antibiotics
sample_data(ps1)$day## [1] -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9
## [24] -9 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7
## [47] 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 0 0 0
## [70] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## [93] 0 0 0 0 0 0 0 0ps1.d.9.narrow <- subset_samples(ps1.narrow, day == "-9")
sample_data(ps1.d.9.narrow)$day## [1] -9 -9 -9 -9 -9 -9 -9 -9
## Levels: -9sample_data(ps1.d.9.narrow)$randomization_arm## [1] Narrow spectrum antibiotics Narrow spectrum antibiotics
## [3] Narrow spectrum antibiotics Narrow spectrum antibiotics
## [5] Narrow spectrum antibiotics Narrow spectrum antibiotics
## [7] Narrow spectrum antibiotics Narrow spectrum antibiotics
## Levels: Narrow spectrum antibiotics# Differential Abundance Testing
ds.d.9.narrow <- phyloseq_to_deseq2(ps1.d.9.narrow, ~d7_rota_boost_updated)
geoMeans.ds.d.9.narrow <- apply(counts(ds.d.9.narrow), 1, gm_mean)
ds.d.9.narrow <- estimateSizeFactors(ds.d.9.narrow, geoMeans = geoMeans.ds.d.9.narrow)
dds.d.9.narrow <- DESeq(ds.d.9.narrow, test="Wald", fitType="local", betaPrior = FALSE)
alpha = 0.05
# Tabulate and write results
res.dds.d.9.narrow = results(dds.d.9.narrow, cooksCutoff = FALSE)
sigtab_dds.dds.d.9.narrow = res.dds.d.9.narrow[which(res.dds.d.9.narrow$padj < alpha), ]
sigtab_dds.dds.d.9.narrow = cbind(as(sigtab_dds.dds.d.9.narrow, "data.frame"), as(tax_table(ps1.d.9.narrow)[rownames(sigtab_dds.dds.d.9.narrow), ], "matrix"))
summary(res.dds.d.9.narrow)##
## out of 469 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up) : 46, 9.8%
## LFC < 0 (down) : 36, 7.7%
## outliers [1] : 0, 0%
## low counts [2] : 159, 34%
## (mean count < 4)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?resultshead(sigtab_dds.dds.d.9.narrow)## baseMean
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 1766.32988
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 212.08362
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT 72.68788
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 195.55351
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT 26.67661
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 48.19724
## log2FoldChange
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT -28.48937
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 24.78646
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT -24.11592
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 24.67326
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT -22.76311
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT -23.56139
## lfcSE
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 3.383398
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 3.383542
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT 3.383988
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 3.383556
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT 3.385049
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 3.384300
## stat
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT -8.420343
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 7.325595
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT -7.126480
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 7.292108
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT -6.724603
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT -6.961968
## pvalue
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 3.753834e-17
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 2.378407e-13
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT 1.029686e-12
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 3.051422e-13
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT 1.760713e-11
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 3.355510e-12
## padj
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 1.163689e-14
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 1.843265e-11
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT 3.546695e-11
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 1.891882e-11
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT 2.274255e-10
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 7.240322e-11
## Kingdom
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteria
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Bacteria
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT Bacteria
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT Bacteria
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT Bacteria
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteria
## Phylum
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidetes
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Firmicutes
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT Firmicutes
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT Firmicutes
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT Firmicutes
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroidetes
## Class
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidia
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Negativicutes
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT Negativicutes
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT Clostridia
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT Negativicutes
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroidia
## Order
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidales
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Selenomonadales
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT Selenomonadales
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT Clostridiales
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT Selenomonadales
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroidales
## Family
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Prevotellaceae
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Veillonellaceae
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT Veillonellaceae
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT Ruminococcaceae
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT Acidaminococcaceae
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroidaceae
## Genus
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Prevotella
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Dialister
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT Megamonas
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT Ruminococcus
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT Phascolarctobacterium
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroides
## Species
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT <NA>
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG <NA>
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT funiformis
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT <NA>
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT faecium
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT doreiwrite.table(sigtab_dds.dds.d.9.narrow, file="./results/deseq_d.9_narrow_rota_boost.txt", sep = "\t") # Change filename to save results to appropriate file
# Quick check of factor levels
mcols(res.dds.d.9.narrow, use.names = TRUE)## DataFrame with 6 rows and 2 columns
## type
## <character>
## baseMean intermediate
## log2FoldChange results
## lfcSE results
## stat results
## pvalue results
## padj results
## description
## <character>
## baseMean mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): d7 rota boost updated Yes vs No
## lfcSE standard error: d7 rota boost updated Yes vs No
## stat Wald statistic: d7 rota boost updated Yes vs No
## pvalue Wald test p-value: d7 rota boost updated Yes vs No
## padj BH adjusted p-values# Prepare to join results data.table and taxonomy table
resdt.dds.d.9.narrow = data.table(as(results(dds.d.9.narrow, cooksCutoff = FALSE), "data.frame"),
keep.rownames = TRUE)
setnames(resdt.dds.d.9.narrow, "rn", "OTU")
taxdt.dds.d.9.com = data.table(data.frame(as(tax_table(ps1.d.9.narrow), "matrix")), keep.rownames = TRUE)
setnames(taxdt.dds.d.9.com, "rn", "OTU")
# Join results data.table and taxonomy table
setkeyv(taxdt.dds.d.9.com, "OTU")
setkeyv(resdt.dds.d.9.narrow, "OTU")
resdt.dds.d.9.narrow <- taxdt.dds.d.9.com[resdt.dds.d.9.narrow]
resdt.dds.d.9.narrow## OTU
## 1: ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 2: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
## 3: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
## 4: ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 5: ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
## ---
## 1586: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
## Kingdom Phylum Class Order
## 1: Bacteria Firmicutes Clostridia Clostridiales
## 2: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 3: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 4: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 5: Bacteria Firmicutes Clostridia Clostridiales
## ---
## 1586: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1587: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1588: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1589: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1590: Archaea Euryarchaeota Methanobacteria Methanobacteriales
## Family Genus Species baseMean
## 1: Ruminococcaceae NA NA 0.000000
## 2: Fusobacteriaceae Fusobacterium nucleatum 0.000000
## 3: Fusobacteriaceae Fusobacterium NA 0.000000
## 4: Rikenellaceae NA NA 0.000000
## 5: Eubacteriaceae Eubacterium NA 0.000000
## ---
## 1586: Bacteroidaceae Bacteroides stercoris 58.270669
## 1587: Bacteroidaceae Bacteroides NA 52.257748
## 1588: Prevotellaceae Prevotella NA 0.000000
## 1589: Prevotellaceae Prevotella bivia 0.000000
## 1590: Methanobacteriaceae Methanobrevibacter NA 4.821277
## log2FoldChange lfcSE stat pvalue padj
## 1: NA NA NA NA NA
## 2: NA NA NA NA NA
## 3: NA NA NA NA NA
## 4: NA NA NA NA NA
## 5: NA NA NA NA NA
## ---
## 1586: -23.82741 3.384139 -7.040908 1.909917e-12 4.933952e-11
## 1587: -23.67565 3.384227 -6.995880 2.635985e-12 6.285811e-11
## 1588: NA NA NA NA NA
## 1589: NA NA NA NA NA
## 1590: 5.60415 3.182472 1.760942 7.824816e-02 2.241558e-01resdt.dds.d.9.narrow[, Significant := padj < alpha]
resdt.dds.d.9.narrow[!is.na(Significant)]## OTU
## 1: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 2: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGTAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 3: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTTAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 4: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 5: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## ---
## 306: TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCGGTTTCGTAAGTCGTGTGTGAAAGGCGGGGGCTCAACCCCCGGACTGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG
## 307: TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG
## 308: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 309: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 310: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
## Kingdom Phylum Class Order
## 1: Bacteria Firmicutes Clostridia Clostridiales
## 2: Bacteria Firmicutes Clostridia Clostridiales
## 3: Bacteria Firmicutes Clostridia Clostridiales
## 4: Bacteria Firmicutes Clostridia Clostridiales
## 5: Bacteria Firmicutes Clostridia Clostridiales
## ---
## 306: Bacteria Verrucomicrobia Verrucomicrobiae Verrucomicrobiales
## 307: Bacteria Verrucomicrobia Verrucomicrobiae Verrucomicrobiales
## 308: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 309: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 310: Archaea Euryarchaeota Methanobacteria Methanobacteriales
## Family Genus Species baseMean
## 1: Ruminococcaceae Faecalibacterium prausnitzii 2195.621485
## 2: Ruminococcaceae Faecalibacterium NA 28.411359
## 3: Ruminococcaceae Faecalibacterium NA 46.137588
## 4: Ruminococcaceae Faecalibacterium prausnitzii 1704.807731
## 5: Ruminococcaceae Faecalibacterium NA 4.517713
## ---
## 306: Verrucomicrobiaceae Akkermansia NA 23.562976
## 307: Verrucomicrobiaceae Akkermansia muciniphila 27.933233
## 308: Bacteroidaceae Bacteroides stercoris 58.270669
## 309: Bacteroidaceae Bacteroides NA 52.257748
## 310: Methanobacteriaceae Methanobrevibacter NA 4.821277
## log2FoldChange lfcSE stat pvalue padj
## 1: 0.4403465 1.654648 0.2661270 7.901414e-01 9.493947e-01
## 2: -22.7125700 3.384945 -6.7098791 1.947857e-11 2.322445e-10
## 3: -9.0755154 3.384341 -2.6816199 7.326665e-03 2.949696e-02
## 4: 0.5329179 1.458388 0.3654157 7.148011e-01 9.436458e-01
## 5: 5.5171402 3.391411 1.6267981 1.037800e-01 2.485223e-01
## ---
## 306: 21.7238114 3.384917 6.4178277 1.382326e-10 1.127687e-09
## 307: 1.6111951 3.234527 0.4981239 6.183967e-01 9.351365e-01
## 308: -23.8274114 3.384139 -7.0409076 1.909917e-12 4.933952e-11
## 309: -23.6756493 3.384227 -6.9958803 2.635985e-12 6.285811e-11
## 310: 5.6041500 3.182472 1.7609424 7.824816e-02 2.241558e-01
## Significant
## 1: FALSE
## 2: TRUE
## 3: TRUE
## 4: FALSE
## 5: FALSE
## ---
## 306: TRUE
## 307: FALSE
## 308: TRUE
## 309: TRUE
## 310: FALSEresdt.dds.d.9.narrow## OTU
## 1: ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 2: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
## 3: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
## 4: ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 5: ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
## ---
## 1586: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
## Kingdom Phylum Class Order
## 1: Bacteria Firmicutes Clostridia Clostridiales
## 2: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 3: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 4: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 5: Bacteria Firmicutes Clostridia Clostridiales
## ---
## 1586: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1587: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1588: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1589: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1590: Archaea Euryarchaeota Methanobacteria Methanobacteriales
## Family Genus Species baseMean
## 1: Ruminococcaceae NA NA 0.000000
## 2: Fusobacteriaceae Fusobacterium nucleatum 0.000000
## 3: Fusobacteriaceae Fusobacterium NA 0.000000
## 4: Rikenellaceae NA NA 0.000000
## 5: Eubacteriaceae Eubacterium NA 0.000000
## ---
## 1586: Bacteroidaceae Bacteroides stercoris 58.270669
## 1587: Bacteroidaceae Bacteroides NA 52.257748
## 1588: Prevotellaceae Prevotella NA 0.000000
## 1589: Prevotellaceae Prevotella bivia 0.000000
## 1590: Methanobacteriaceae Methanobrevibacter NA 4.821277
## log2FoldChange lfcSE stat pvalue padj
## 1: NA NA NA NA NA
## 2: NA NA NA NA NA
## 3: NA NA NA NA NA
## 4: NA NA NA NA NA
## 5: NA NA NA NA NA
## ---
## 1586: -23.82741 3.384139 -7.040908 1.909917e-12 4.933952e-11
## 1587: -23.67565 3.384227 -6.995880 2.635985e-12 6.285811e-11
## 1588: NA NA NA NA NA
## 1589: NA NA NA NA NA
## 1590: 5.60415 3.182472 1.760942 7.824816e-02 2.241558e-01
## Significant
## 1: NA
## 2: NA
## 3: NA
## 4: NA
## 5: NA
## ---
## 1586: TRUE
## 1587: TRUE
## 1588: NA
## 1589: NA
## 1590: FALSEvolcano.d.9.narrow.boost = ggplot(
data = resdt.dds.d.9.narrow[!is.na(Significant)][(pvalue < 1)],
mapping = aes(x = log2FoldChange,
y = -log10(pvalue),
color = Phylum,
label = OTU, label1 = Genus)) +
theme_bw() +
geom_point() +
geom_point(data = resdt.dds.d.9.narrow[(Significant)], size = 7, alpha = 0.7) +
# geom_text(data = resdt[(Significant)], mapping = aes(label = paste("Genus:", Genus)), color = "black", size = 3) +
theme(axis.text.x = element_text(angle = -90, hjust = 0, vjust=0.5)) +
geom_hline(yintercept = -log10(alpha)) +
ggtitle("DESeq2 Negative Binomial Test Volcano Plot\nDay -9 Narrow Spectrum Antibiotics ~ Rotavirus Boost") +
theme(axis.title = element_text(size=12)) +
theme(axis.text = element_text(size=12)) +
theme(legend.text = element_text(size=12)) +
geom_vline(xintercept = 0, lty = 2)
volcano.d.9.narrow.boost
summary(res.dds.d.9.narrow)##
## out of 469 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up) : 46, 9.8%
## LFC < 0 (down) : 36, 7.7%
## outliers [1] : 0, 0%
## low counts [2] : 159, 34%
## (mean count < 4)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?resultsmcols(res.dds.d.9.narrow, use.names = TRUE)## DataFrame with 6 rows and 2 columns
## type
## <character>
## baseMean intermediate
## log2FoldChange results
## lfcSE results
## stat results
## pvalue results
## padj results
## description
## <character>
## baseMean mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): d7 rota boost updated Yes vs No
## lfcSE standard error: d7 rota boost updated Yes vs No
## stat Wald statistic: d7 rota boost updated Yes vs No
## pvalue Wald test p-value: d7 rota boost updated Yes vs No
## padj BH adjusted p-valuesggplotly(volcano.d.9.narrow.boost)BOOST: Day 0 Narrow Spectrum Antibiotics
sample_data(ps1)$day## [1] -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9
## [24] -9 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7
## [47] 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 0 0 0
## [70] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## [93] 0 0 0 0 0 0 0 0ps1.d0.narrow <- subset_samples(ps1.narrow, day == "0")
sample_data(ps1.d0.narrow)$day## [1] 0 0 0 0 0 0 0 0 0 0 0 0 0
## Levels: 0sample_data(ps1.d0.narrow)$randomization_arm## [1] Narrow spectrum antibiotics Narrow spectrum antibiotics
## [3] Narrow spectrum antibiotics Narrow spectrum antibiotics
## [5] Narrow spectrum antibiotics Narrow spectrum antibiotics
## [7] Narrow spectrum antibiotics Narrow spectrum antibiotics
## [9] Narrow spectrum antibiotics Narrow spectrum antibiotics
## [11] Narrow spectrum antibiotics Narrow spectrum antibiotics
## [13] Narrow spectrum antibiotics
## Levels: Narrow spectrum antibiotics# Differential Abundance Testing
ds.d0.narrow <- phyloseq_to_deseq2(ps1.d0.narrow, ~d7_rota_boost_updated)
geoMeans.ds.d0.narrow <- apply(counts(ds.d0.narrow), 1, gm_mean)
ds.d0.narrow <- estimateSizeFactors(ds.d0.narrow, geoMeans = geoMeans.ds.d0.narrow)
dds.d0.narrow <- DESeq(ds.d0.narrow, test="Wald", fitType="local", betaPrior = FALSE)
alpha = 0.05
# Tabulate and write results
res.dds.d0.narrow = results(dds.d0.narrow, cooksCutoff = FALSE)
sigtab_dds.dds.d0.narrow = res.dds.d0.narrow[which(res.dds.d0.narrow$padj < alpha), ]
sigtab_dds.dds.d0.narrow = cbind(as(sigtab_dds.dds.d0.narrow, "data.frame"), as(tax_table(ps1.d0.narrow)[rownames(sigtab_dds.dds.d0.narrow), ], "matrix"))
summary(res.dds.d0.narrow)##
## out of 182 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up) : 36, 20%
## LFC < 0 (down) : 4, 2.2%
## outliers [1] : 0, 0%
## low counts [2] : 130, 71%
## (mean count < 1)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?resultshead(sigtab_dds.dds.d0.narrow)## baseMean
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 703.511301
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG 4.606087
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT 6.889104
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 18.784824
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT 139.684130
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC 1047.916550
## log2FoldChange
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 9.034369
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG 20.603394
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT 21.161672
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 22.552152
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT 25.349818
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC 26.872310
## lfcSE
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 2.912451
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG 3.002982
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT 3.000332
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 2.996913
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT 2.995183
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC 2.994950
## stat
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 3.101982
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG 6.860979
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT 7.053109
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 7.525129
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT 8.463528
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC 8.972541
## pvalue
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 1.922300e-03
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG 6.839046e-12
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT 1.749632e-12
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 5.266844e-14
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT 2.594085e-17
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC 2.897503e-19
## padj
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 5.999905e-03
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG 2.709314e-11
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT 9.010606e-12
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 5.413726e-13
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT 8.906360e-16
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC 2.403841e-17
## Kingdom
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteria
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG Bacteria
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT Bacteria
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteria
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT Bacteria
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC Bacteria
## Phylum
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidetes
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG Firmicutes
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT Bacteroidetes
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroidetes
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT Firmicutes
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC Synergistetes
## Class
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidia
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG Clostridia
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT Bacteroidia
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroidia
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT Negativicutes
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC Synergistia
## Order
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidales
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG Clostridiales
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT Bacteroidales
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroidales
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT Selenomonadales
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC Synergistales
## Family
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Prevotellaceae
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG Lachnospiraceae
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT Bacteroidaceae
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroidaceae
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT Acidaminococcaceae
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC Synergistaceae
## Genus
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Prevotella
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG Blautia
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT Bacteroides
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroides
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT Acidaminococcus
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC Cloacibacillus
## Species
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT copri
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG <NA>
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT ovatus
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT dorei
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT <NA>
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC evryensiswrite.table(sigtab_dds.dds.d0.narrow, file="./results/deseq_d7_narrow_rota_boost.txt", sep = "\t") # Change filename to save results to appropriate file
# Quick check of factor levels
mcols(res.dds.d0.narrow, use.names = TRUE)## DataFrame with 6 rows and 2 columns
## type
## <character>
## baseMean intermediate
## log2FoldChange results
## lfcSE results
## stat results
## pvalue results
## padj results
## description
## <character>
## baseMean mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): d7 rota boost updated Yes vs No
## lfcSE standard error: d7 rota boost updated Yes vs No
## stat Wald statistic: d7 rota boost updated Yes vs No
## pvalue Wald test p-value: d7 rota boost updated Yes vs No
## padj BH adjusted p-values# Prepare to join results data.table and taxonomy table
resdt.dds.d0.narrow = data.table(as(results(dds.d0.narrow, cooksCutoff = FALSE), "data.frame"),
keep.rownames = TRUE)
setnames(resdt.dds.d0.narrow, "rn", "OTU")
taxdt.dds.d0.com = data.table(data.frame(as(tax_table(ps1.d0.narrow), "matrix")), keep.rownames = TRUE)
setnames(taxdt.dds.d0.com, "rn", "OTU")
# Join results data.table and taxonomy table
setkeyv(taxdt.dds.d0.com, "OTU")
setkeyv(resdt.dds.d0.narrow, "OTU")
resdt.dds.d0.narrow <- taxdt.dds.d0.com[resdt.dds.d0.narrow]
resdt.dds.d0.narrow## OTU
## 1: ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 2: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
## 3: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
## 4: ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 5: ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
## ---
## 1586: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
## Kingdom Phylum Class Order
## 1: Bacteria Firmicutes Clostridia Clostridiales
## 2: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 3: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 4: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 5: Bacteria Firmicutes Clostridia Clostridiales
## ---
## 1586: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1587: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1588: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1589: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1590: Archaea Euryarchaeota Methanobacteria Methanobacteriales
## Family Genus Species baseMean
## 1: Ruminococcaceae NA NA 0.0000000
## 2: Fusobacteriaceae Fusobacterium nucleatum 0.0000000
## 3: Fusobacteriaceae Fusobacterium NA 0.3496783
## 4: Rikenellaceae NA NA 0.0000000
## 5: Eubacteriaceae Eubacterium NA 0.0000000
## ---
## 1586: Bacteroidaceae Bacteroides stercoris 0.0000000
## 1587: Bacteroidaceae Bacteroides NA 0.0000000
## 1588: Prevotellaceae Prevotella NA 0.0000000
## 1589: Prevotellaceae Prevotella bivia 2.6389631
## 1590: Methanobacteriaceae Methanobrevibacter NA 7.1099698
## log2FoldChange lfcSE stat pvalue padj
## 1: NA NA NA NA NA
## 2: NA NA NA NA NA
## 3: -1.711694 3.066810 -0.5581352 0.57675209 NA
## 4: NA NA NA NA NA
## 5: NA NA NA NA NA
## ---
## 1586: NA NA NA NA NA
## 1587: NA NA NA NA NA
## 1588: NA NA NA NA NA
## 1589: -4.497915 3.013771 -1.4924542 0.13558011 0.23669071
## 1590: 6.507048 3.000192 2.1688775 0.03009199 0.08156512resdt.dds.d0.narrow[, Significant := padj < alpha]
resdt.dds.d0.narrow[!is.na(Significant)]## OTU
## 1: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAGAACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 2: CCAGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGCCCCTTAAGCGTGTTGTGAAATGCCGCGGCTCAACCGTGGCACTGCAGCGCGAACTGGGGGGCTTGAGTGCACGCAACGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTGCGGGAGTGCGACTGACGCTGAAGCTCGAAGGTGCGGGT
## 3: CCAGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGCCCCTTAAGCGTGTTGTGAAATGCCGCGGCTCAACCGTGGCACTGCAGCGCGAACTGGGGGGCTTGAGTGCACGCAACGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGTAGCTTGCGGGAGTGCGACTGACGCTGAAGCTCGAAGGTGCGGGT
## 4: CCAGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGCCCCTTAAGCGTGTTGTGAAATGCCGCGGCTCAACCGTGGCACTGCAGCGCGAACTGGGGGGCTTGAGTGCACGCAACGCAGGTGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTGCGGGAGTGCGACTGACGCTGAAGCTCGAAGGTGCGGGT
## 5: CCAGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCTGGAGATTAAGTGTGTTGTGAAATGTAGACGCTCAACGTCTGAATTGCAGCGCATACTGGTTTCCTTGAGTACGCACAACGTTGGCGGAATTCGTCGTGTAGCGGTGAAATGCTTAGATATGACGAAGAACTCCGATTGCGAAGGCAGCTGACGGGAGCGCAACTGACGCTTAAGCTCGAAGGTGCGGGT
## ---
## 99: TCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTGATAAGTTAGAGGTGAAATCCCGGGGCTTAACTCCGGAACTGCCTCTAATACTGTTAGACTAGAGAGTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCTTAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTATATCTGACGTTGAGGCACGAAAGCGTGGGG
## 100: TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCGGTTTCGTAAGTCGTGTGTGAAAGGCGGGGGCTCAACCCCCGGACTGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG
## 101: TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG
## 102: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 103: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
## Kingdom Phylum Class Order
## 1: Bacteria Firmicutes Clostridia Clostridiales
## 2: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 3: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 4: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 5: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## ---
## 99: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 100: Bacteria Verrucomicrobia Verrucomicrobiae Verrucomicrobiales
## 101: Bacteria Verrucomicrobia Verrucomicrobiae Verrucomicrobiales
## 102: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 103: Archaea Euryarchaeota Methanobacteria Methanobacteriales
## Family Genus Species baseMean
## 1: Ruminococcaceae Faecalibacterium prausnitzii 3.134710
## 2: Prevotellaceae Prevotella NA 15.059902
## 3: Prevotellaceae Prevotella NA 7.069342
## 4: Prevotellaceae Prevotella NA 15.320246
## 5: Prevotellaceae Prevotella melaninogenica 4.500581
## ---
## 99: Rikenellaceae Alistipes NA 2.182885
## 100: Verrucomicrobiaceae Akkermansia NA 370.893878
## 101: Verrucomicrobiaceae Akkermansia muciniphila 1514.314987
## 102: Prevotellaceae Prevotella bivia 2.638963
## 103: Methanobacteriaceae Methanobrevibacter NA 7.109970
## log2FoldChange lfcSE stat pvalue padj
## 1: 5.3287520 3.006810 1.7722278 7.635674e-02 1.747721e-01
## 2: 20.7492055 2.997405 6.9223889 4.440902e-12 1.905887e-11
## 3: 19.6246997 3.000196 6.5411383 6.105234e-11 2.028513e-10
## 4: 22.2698847 2.997363 7.4298266 1.087401e-13 8.000167e-13
## 5: -1.5595525 2.940371 -0.5303932 5.958394e-01 6.941314e-01
## ---
## 99: 4.8284659 3.011690 1.6032412 1.088814e-01 2.156690e-01
## 100: 26.7151976 2.995015 8.9198867 4.667653e-19 2.403841e-17
## 101: -0.5705423 2.894036 -0.1971442 8.437147e-01 8.959033e-01
## 102: -4.4979152 3.013771 -1.4924542 1.355801e-01 2.366907e-01
## 103: 6.5070483 3.000192 2.1688775 3.009199e-02 8.156512e-02
## Significant
## 1: FALSE
## 2: TRUE
## 3: TRUE
## 4: TRUE
## 5: FALSE
## ---
## 99: FALSE
## 100: TRUE
## 101: FALSE
## 102: FALSE
## 103: FALSEresdt.dds.d0.narrow## OTU
## 1: ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 2: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
## 3: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
## 4: ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 5: ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
## ---
## 1586: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
## Kingdom Phylum Class Order
## 1: Bacteria Firmicutes Clostridia Clostridiales
## 2: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 3: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 4: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 5: Bacteria Firmicutes Clostridia Clostridiales
## ---
## 1586: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1587: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1588: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1589: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1590: Archaea Euryarchaeota Methanobacteria Methanobacteriales
## Family Genus Species baseMean
## 1: Ruminococcaceae NA NA 0.0000000
## 2: Fusobacteriaceae Fusobacterium nucleatum 0.0000000
## 3: Fusobacteriaceae Fusobacterium NA 0.3496783
## 4: Rikenellaceae NA NA 0.0000000
## 5: Eubacteriaceae Eubacterium NA 0.0000000
## ---
## 1586: Bacteroidaceae Bacteroides stercoris 0.0000000
## 1587: Bacteroidaceae Bacteroides NA 0.0000000
## 1588: Prevotellaceae Prevotella NA 0.0000000
## 1589: Prevotellaceae Prevotella bivia 2.6389631
## 1590: Methanobacteriaceae Methanobrevibacter NA 7.1099698
## log2FoldChange lfcSE stat pvalue padj Significant
## 1: NA NA NA NA NA NA
## 2: NA NA NA NA NA NA
## 3: -1.711694 3.066810 -0.5581352 0.57675209 NA NA
## 4: NA NA NA NA NA NA
## 5: NA NA NA NA NA NA
## ---
## 1586: NA NA NA NA NA NA
## 1587: NA NA NA NA NA NA
## 1588: NA NA NA NA NA NA
## 1589: -4.497915 3.013771 -1.4924542 0.13558011 0.23669071 FALSE
## 1590: 6.507048 3.000192 2.1688775 0.03009199 0.08156512 FALSEvolcano.d0.narrow.boost = ggplot(
data = resdt.dds.d0.narrow[!is.na(Significant)][(pvalue < 1)],
mapping = aes(x = log2FoldChange,
y = -log10(pvalue),
color = Phylum,
label = OTU, label1 = Genus)) +
theme_bw() +
geom_point() +
geom_point(data = resdt.dds.d0.narrow[(Significant)], size = 7, alpha = 0.7) +
# geom_text(data = resdt[(Significant)], mapping = aes(label = paste("Genus:", Genus)), color = "black", size = 3) +
theme(axis.text.x = element_text(angle = -90, hjust = 0, vjust=0.5)) +
geom_hline(yintercept = -log10(alpha)) +
ggtitle("DESeq2 Negative Binomial Test Volcano Plot\nDay 0 Narrow Spectrum Antibiotics ~ Rotavirus Boost") +
theme(axis.title = element_text(size=12)) +
theme(axis.text = element_text(size=12)) +
theme(legend.text = element_text(size=12)) +
geom_vline(xintercept = 0, lty = 2)
volcano.d0.narrow.boost
summary(res.dds.d0.narrow)##
## out of 182 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up) : 36, 20%
## LFC < 0 (down) : 4, 2.2%
## outliers [1] : 0, 0%
## low counts [2] : 130, 71%
## (mean count < 1)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?resultsmcols(res.dds.d0.narrow, use.names = TRUE)## DataFrame with 6 rows and 2 columns
## type
## <character>
## baseMean intermediate
## log2FoldChange results
## lfcSE results
## stat results
## pvalue results
## padj results
## description
## <character>
## baseMean mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): d7 rota boost updated Yes vs No
## lfcSE standard error: d7 rota boost updated Yes vs No
## stat Wald statistic: d7 rota boost updated Yes vs No
## pvalue Wald test p-value: d7 rota boost updated Yes vs No
## padj BH adjusted p-valuesggplotly(volcano.d0.narrow.boost)BOOST: Day 7 Narrow Spectrum Antibiotics
sample_data(ps1)$day## [1] -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9
## [24] -9 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7
## [47] 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 0 0 0
## [70] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## [93] 0 0 0 0 0 0 0 0ps1.d7.narrow <- subset_samples(ps1.narrow, day == "7")
sample_data(ps1.d7.narrow)$day## [1] 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7
## Levels: 7sample_data(ps1.d7.narrow)$randomization_arm## [1] Narrow spectrum antibiotics Narrow spectrum antibiotics
## [3] Narrow spectrum antibiotics Narrow spectrum antibiotics
## [5] Narrow spectrum antibiotics Narrow spectrum antibiotics
## [7] Narrow spectrum antibiotics Narrow spectrum antibiotics
## [9] Narrow spectrum antibiotics Narrow spectrum antibiotics
## [11] Narrow spectrum antibiotics Narrow spectrum antibiotics
## [13] Narrow spectrum antibiotics Narrow spectrum antibiotics
## [15] Narrow spectrum antibiotics
## Levels: Narrow spectrum antibiotics# Differential Abundance Testing
ds.d7.narrow <- phyloseq_to_deseq2(ps1.d7.narrow, ~d7_rota_boost_updated)
geoMeans.ds.d7.narrow <- apply(counts(ds.d7.narrow), 1, gm_mean)
ds.d7.narrow <- estimateSizeFactors(ds.d7.narrow, geoMeans = geoMeans.ds.d7.narrow)
dds.d7.narrow <- DESeq(ds.d7.narrow, test="Wald", fitType="local", betaPrior = FALSE)
alpha = 0.05
# Tabulate and write results
res.dds.d7.narrow = results(dds.d7.narrow, cooksCutoff = FALSE)
sigtab_dds.dds.d7.narrow = res.dds.d7.narrow[which(res.dds.d7.narrow$padj < alpha), ]
sigtab_dds.dds.d7.narrow = cbind(as(sigtab_dds.dds.d7.narrow, "data.frame"), as(tax_table(ps1.d7.narrow)[rownames(sigtab_dds.dds.d7.narrow), ], "matrix"))
summary(res.dds.d7.narrow)##
## out of 538 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up) : 160, 30%
## LFC < 0 (down) : 16, 3%
## outliers [1] : 0, 0%
## low counts [2] : 379, 70%
## (mean count < 3)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?resultshead(sigtab_dds.dds.d7.narrow)## baseMean
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 2897.92173
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 1047.66115
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT 172.92756
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 343.72024
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 42.07216
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGGTCGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 71.32087
## log2FoldChange
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 11.278714
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 28.626919
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT -25.437960
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 26.344992
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 24.028972
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGGTCGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 7.212213
## lfcSE
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 2.958993
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 3.022391
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT 3.060524
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 3.022442
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 3.022981
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGGTCGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 2.648139
## stat
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 3.811673
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 9.471613
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT -8.311635
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 8.716460
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 7.948766
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGGTCGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 2.723503
## pvalue
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 1.380297e-04
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 2.755559e-21
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT 9.439256e-17
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 2.870359e-18
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 1.883782e-15
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGGTCGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 6.459372e-03
## padj
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 4.090237e-04
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 8.900455e-19
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT 2.771709e-15
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 3.090420e-16
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 2.535256e-14
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGGTCGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 1.783228e-02
## Kingdom
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteria
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Bacteria
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT Bacteria
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT Bacteria
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteria
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGGTCGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Bacteria
## Phylum
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidetes
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Firmicutes
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT Fusobacteria
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT Firmicutes
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroidetes
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGGTCGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Firmicutes
## Class
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidia
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Negativicutes
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT Fusobacteriia
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT Clostridia
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroidia
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGGTCGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Clostridia
## Order
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidales
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Selenomonadales
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT Fusobacteriales
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT Clostridiales
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroidales
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGGTCGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Clostridiales
## Family
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Prevotellaceae
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Veillonellaceae
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT Fusobacteriaceae
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT Ruminococcaceae
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroidaceae
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGGTCGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Ruminococcaceae
## Genus
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Prevotella
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Dialister
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT Fusobacterium
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT Ruminococcus
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroides
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGGTCGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Faecalibacterium
## Species
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT <NA>
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG <NA>
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT <NA>
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT <NA>
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATGTCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT dorei
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGGTCGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT prausnitziiwrite.table(sigtab_dds.dds.d7.narrow, file="./results/deseq_d7_narrow_rota_boost.txt", sep = "\t") # Change filename to save results to appropriate file
# Quick check of factor levels
mcols(res.dds.d7.narrow, use.names = TRUE)## DataFrame with 6 rows and 2 columns
## type
## <character>
## baseMean intermediate
## log2FoldChange results
## lfcSE results
## stat results
## pvalue results
## padj results
## description
## <character>
## baseMean mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): d7 rota boost updated Yes vs No
## lfcSE standard error: d7 rota boost updated Yes vs No
## stat Wald statistic: d7 rota boost updated Yes vs No
## pvalue Wald test p-value: d7 rota boost updated Yes vs No
## padj BH adjusted p-values# Prepare to join results data.table and taxonomy table
resdt.dds.d7.narrow = data.table(as(results(dds.d7.narrow, cooksCutoff = FALSE), "data.frame"),
keep.rownames = TRUE)
setnames(resdt.dds.d7.narrow, "rn", "OTU")
taxdt.dds.d7.com = data.table(data.frame(as(tax_table(ps1.d7.narrow), "matrix")), keep.rownames = TRUE)
setnames(taxdt.dds.d7.com, "rn", "OTU")
# Join results data.table and taxonomy table
setkeyv(taxdt.dds.d7.com, "OTU")
setkeyv(resdt.dds.d7.narrow, "OTU")
resdt.dds.d7.narrow <- taxdt.dds.d7.com[resdt.dds.d7.narrow]
resdt.dds.d7.narrow## OTU
## 1: ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 2: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
## 3: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
## 4: ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 5: ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
## ---
## 1586: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
## Kingdom Phylum Class Order
## 1: Bacteria Firmicutes Clostridia Clostridiales
## 2: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 3: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 4: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 5: Bacteria Firmicutes Clostridia Clostridiales
## ---
## 1586: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1587: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1588: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1589: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1590: Archaea Euryarchaeota Methanobacteria Methanobacteriales
## Family Genus Species baseMean
## 1: Ruminococcaceae NA NA 0.000000
## 2: Fusobacteriaceae Fusobacterium nucleatum 0.000000
## 3: Fusobacteriaceae Fusobacterium NA 0.000000
## 4: Rikenellaceae NA NA 0.000000
## 5: Eubacteriaceae Eubacterium NA 0.000000
## ---
## 1586: Bacteroidaceae Bacteroides stercoris 0.000000
## 1587: Bacteroidaceae Bacteroides NA 0.000000
## 1588: Prevotellaceae Prevotella NA 28.552648
## 1589: Prevotellaceae Prevotella bivia 0.000000
## 1590: Methanobacteriaceae Methanobrevibacter NA 3.401384
## log2FoldChange lfcSE stat pvalue padj
## 1: NA NA NA NA NA
## 2: 0.000000 0.000000 0.000000 1.000000e+00 NA
## 3: NA NA NA NA NA
## 4: NA NA NA NA NA
## 5: NA NA NA NA NA
## ---
## 1586: NA NA NA NA NA
## 1587: NA NA NA NA NA
## 1588: 23.590829 3.023272 7.803079 6.041479e-15 6.366766e-14
## 1589: NA NA NA NA NA
## 1590: 3.813212 3.015695 1.264455 2.060666e-01 2.856632e-01resdt.dds.d7.narrow[, Significant := padj < alpha]
resdt.dds.d7.narrow[!is.na(Significant)]## OTU
## 1: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 2: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 3: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGATAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 4: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAGAACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 5: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTATGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## ---
## 319: TCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTGATAAGTTAGAGGTGAAATCCCGGGGCTTAACTCCGGAACTGCCTCTAATACTGTTAGACTAGAGAGTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCTTAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTATATCTGACGTTGAGGCACGAAAGCGTGGGG
## 320: TCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTGATAAGTTAGAGGTGAAATTTCGGGGCTCAACCCTGAACGTGCCTCTAATACTGTTGAGCTAGAGAGTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCTTAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTATATCTGACGTTGAGGCACGAAAGCGTGGGG
## 321: TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG
## 322: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 323: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
## Kingdom Phylum Class Order
## 1: Bacteria Firmicutes Clostridia Clostridiales
## 2: Bacteria Firmicutes Clostridia Clostridiales
## 3: Bacteria Firmicutes Clostridia Clostridiales
## 4: Bacteria Firmicutes Clostridia Clostridiales
## 5: Bacteria Firmicutes Clostridia Clostridiales
## ---
## 319: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 320: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 321: Bacteria Verrucomicrobia Verrucomicrobiae Verrucomicrobiales
## 322: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 323: Archaea Euryarchaeota Methanobacteria Methanobacteriales
## Family Genus Species baseMean
## 1: Ruminococcaceae Faecalibacterium prausnitzii 732.822816
## 2: Ruminococcaceae Faecalibacterium prausnitzii 1160.314775
## 3: Ruminococcaceae Faecalibacterium NA 8.445825
## 4: Ruminococcaceae Faecalibacterium prausnitzii 134.830487
## 5: Ruminococcaceae Faecalibacterium NA 2.687308
## ---
## 319: Rikenellaceae Alistipes NA 8.007783
## 320: Rikenellaceae Alistipes putredinis 47.151212
## 321: Verrucomicrobiaceae Akkermansia muciniphila 3634.940803
## 322: Prevotellaceae Prevotella NA 28.552648
## 323: Methanobacteriaceae Methanobrevibacter NA 3.401384
## log2FoldChange lfcSE stat pvalue padj
## 1: 5.7268242 2.946129 1.9438472 5.191388e-02 9.891567e-02
## 2: -0.6759581 2.689203 -0.2513601 8.015357e-01 8.598082e-01
## 3: 21.8940007 3.025423 7.2366751 4.598178e-13 1.856514e-12
## 4: 4.5457648 2.681134 1.6954632 8.998758e-02 1.345648e-01
## 5: 5.2675987 3.031928 1.7373759 8.232085e-02 1.254228e-01
## ---
## 319: 0.5810587 2.957649 0.1964596 8.442504e-01 8.882504e-01
## 320: 7.0543802 2.989416 2.3597853 1.828551e-02 4.724977e-02
## 321: -0.9299005 2.733387 -0.3402008 7.337053e-01 8.060776e-01
## 322: 23.5908286 3.023272 7.8030788 6.041479e-15 6.366766e-14
## 323: 3.8132121 3.015695 1.2644553 2.060666e-01 2.856632e-01
## Significant
## 1: FALSE
## 2: FALSE
## 3: TRUE
## 4: FALSE
## 5: FALSE
## ---
## 319: FALSE
## 320: TRUE
## 321: FALSE
## 322: TRUE
## 323: FALSEresdt.dds.d7.narrow## OTU
## 1: ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 2: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
## 3: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
## 4: ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 5: ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
## ---
## 1586: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
## Kingdom Phylum Class Order
## 1: Bacteria Firmicutes Clostridia Clostridiales
## 2: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 3: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 4: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 5: Bacteria Firmicutes Clostridia Clostridiales
## ---
## 1586: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1587: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1588: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1589: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1590: Archaea Euryarchaeota Methanobacteria Methanobacteriales
## Family Genus Species baseMean
## 1: Ruminococcaceae NA NA 0.000000
## 2: Fusobacteriaceae Fusobacterium nucleatum 0.000000
## 3: Fusobacteriaceae Fusobacterium NA 0.000000
## 4: Rikenellaceae NA NA 0.000000
## 5: Eubacteriaceae Eubacterium NA 0.000000
## ---
## 1586: Bacteroidaceae Bacteroides stercoris 0.000000
## 1587: Bacteroidaceae Bacteroides NA 0.000000
## 1588: Prevotellaceae Prevotella NA 28.552648
## 1589: Prevotellaceae Prevotella bivia 0.000000
## 1590: Methanobacteriaceae Methanobrevibacter NA 3.401384
## log2FoldChange lfcSE stat pvalue padj
## 1: NA NA NA NA NA
## 2: 0.000000 0.000000 0.000000 1.000000e+00 NA
## 3: NA NA NA NA NA
## 4: NA NA NA NA NA
## 5: NA NA NA NA NA
## ---
## 1586: NA NA NA NA NA
## 1587: NA NA NA NA NA
## 1588: 23.590829 3.023272 7.803079 6.041479e-15 6.366766e-14
## 1589: NA NA NA NA NA
## 1590: 3.813212 3.015695 1.264455 2.060666e-01 2.856632e-01
## Significant
## 1: NA
## 2: NA
## 3: NA
## 4: NA
## 5: NA
## ---
## 1586: NA
## 1587: NA
## 1588: TRUE
## 1589: NA
## 1590: FALSEvolcano.d7.narrow.boost = ggplot(
data = resdt.dds.d7.narrow[!is.na(Significant)][(pvalue < 1)],
mapping = aes(x = log2FoldChange,
y = -log10(pvalue),
color = Phylum,
label = OTU, label1 = Genus)) +
theme_bw() +
geom_point() +
geom_point(data = resdt.dds.d7.narrow[(Significant)], size = 7, alpha = 0.7) +
# geom_text(data = resdt[(Significant)], mapping = aes(label = paste("Genus:", Genus)), color = "black", size = 3) +
theme(axis.text.x = element_text(angle = -90, hjust = 0, vjust=0.5)) +
geom_hline(yintercept = -log10(alpha)) +
ggtitle("DESeq2 Negative Binomial Test Volcano Plot\nDay 7 Narrow Spectrum Antibiotics ~ Rotavirus Boost") +
theme(axis.title = element_text(size=12)) +
theme(axis.text = element_text(size=12)) +
theme(legend.text = element_text(size=12)) +
geom_vline(xintercept = 0, lty = 2)
volcano.d7.narrow.boost
summary(res.dds.d7.narrow)##
## out of 538 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up) : 160, 30%
## LFC < 0 (down) : 16, 3%
## outliers [1] : 0, 0%
## low counts [2] : 379, 70%
## (mean count < 3)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?resultsmcols(res.dds.d7.narrow, use.names = TRUE)## DataFrame with 6 rows and 2 columns
## type
## <character>
## baseMean intermediate
## log2FoldChange results
## lfcSE results
## stat results
## pvalue results
## padj results
## description
## <character>
## baseMean mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): d7 rota boost updated Yes vs No
## lfcSE standard error: d7 rota boost updated Yes vs No
## stat Wald statistic: d7 rota boost updated Yes vs No
## pvalue Wald test p-value: d7 rota boost updated Yes vs No
## padj BH adjusted p-valuesggplotly(volcano.d7.narrow.boost)grid.arrange(volcano.d.9.narrow.boost, volcano.d0.narrow.boost, volcano.d7.narrow.boost, ncol = 3)
Shedding
Shedding: Day -9 Narrow Spectrum Antibiotics
# Differential Abundance Testing
ds.d.9.narrow.shed <- phyloseq_to_deseq2(ps1.d.9.narrow, ~Shedding)
geoMeans.ds.d.9.narrow.shed <- apply(counts(ds.d.9.narrow.shed), 1, gm_mean)
ds.d.9.narrow.shed <- estimateSizeFactors(ds.d.9.narrow.shed, geoMeans = geoMeans.ds.d.9.narrow.shed)
dds.d.9.narrow.shed <- DESeq(ds.d.9.narrow.shed, test="Wald", fitType="local", betaPrior = FALSE)
alpha = 0.05
# Tabulate and write results
res.dds.d.9.narrow.shed = results(dds.d.9.narrow.shed, cooksCutoff = FALSE)
sigtab_dds.dds.d.9.narrow.shed = res.dds.d.9.narrow.shed[which(res.dds.d.9.narrow.shed$padj < alpha), ]
sigtab_dds.dds.d.9.narrow.shed = cbind(as(sigtab_dds.dds.d.9.narrow.shed, "data.frame"), as(tax_table(ps1.d.9.narrow)[rownames(sigtab_dds.dds.d.9.narrow.shed), ], "matrix"))
summary(res.dds.d.9.narrow.shed)##
## out of 469 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up) : 24, 5.1%
## LFC < 0 (down) : 70, 15%
## outliers [1] : 0, 0%
## low counts [2] : 135, 29%
## (mean count < 3)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?resultshead(sigtab_dds.dds.d.9.narrow.shed)## baseMean
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 1766.32988
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 212.08362
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT 72.68788
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT 71.09135
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 181.72015
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT 26.67661
## log2FoldChange
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 28.71103
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG -24.39424
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT 10.29535
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT -22.90626
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT -24.19062
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT 22.85897
## lfcSE
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 3.454425
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 3.533967
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT 3.455110
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT 3.534263
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 3.533992
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT 3.456344
## stat
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 8.311378
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG -6.902792
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT 2.979746
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT -6.481198
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT -6.845127
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT 6.613627
## pvalue
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 9.459736e-17
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 5.099043e-12
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT 2.884876e-03
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT 9.099746e-11
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 7.640795e-12
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT 3.750147e-11
## padj
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 3.159552e-14
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 2.838467e-10
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT 1.160902e-02
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT 1.321441e-09
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 3.190032e-10
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT 7.828433e-10
## Kingdom
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteria
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Bacteria
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT Bacteria
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT Bacteria
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Bacteria
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT Bacteria
## Phylum
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidetes
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Firmicutes
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT Firmicutes
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT Bacteroidetes
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Firmicutes
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT Firmicutes
## Class
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidia
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Negativicutes
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT Negativicutes
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT Bacteroidia
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Clostridia
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT Negativicutes
## Order
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidales
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Selenomonadales
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT Selenomonadales
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT Bacteroidales
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Clostridiales
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT Selenomonadales
## Family
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Prevotellaceae
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Veillonellaceae
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT Veillonellaceae
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT Bacteroidaceae
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Ruminococcaceae
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT Acidaminococcaceae
## Genus
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Prevotella
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Dialister
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT Megamonas
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT Bacteroides
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Faecalibacterium
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT Phascolarctobacterium
## Species
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT <NA>
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG <NA>
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT funiformis
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTCACTGACACTGATGCTCGAAAGTGTGGGT ovatus
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT prausnitzii
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGCTTAATAAGTCGAGCGTGAAAATGCGGGGCTCAACCCCGTATGGCGCTGGAAACTGTTAGGCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT faeciumwrite.table(sigtab_dds.dds.d.9.narrow.shed, file="./results/deseq_d.9_narrow_Shedding.txt", sep = "\t") # Change filename to save results to appropriate file
# Quick check of factor levels
mcols(res.dds.d.9.narrow.shed, use.names = TRUE)## DataFrame with 6 rows and 2 columns
## type
## <character>
## baseMean intermediate
## log2FoldChange results
## lfcSE results
## stat results
## pvalue results
## padj results
## description
## <character>
## baseMean mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): Shedding Shedding vs No.shedding
## lfcSE standard error: Shedding Shedding vs No.shedding
## stat Wald statistic: Shedding Shedding vs No.shedding
## pvalue Wald test p-value: Shedding Shedding vs No.shedding
## padj BH adjusted p-values# Prepare to join results data.table and taxonomy table
resdt.dds.d.9.narrow.shed = data.table(as(results(dds.d.9.narrow.shed, cooksCutoff = FALSE), "data.frame"),
keep.rownames = TRUE)
setnames(resdt.dds.d.9.narrow.shed, "rn", "OTU")
taxdt.dds.d.9.com = data.table(data.frame(as(tax_table(ps1.d.9.narrow), "matrix")), keep.rownames = TRUE)
setnames(taxdt.dds.d.9.com, "rn", "OTU")
# Join results data.table and taxonomy table
setkeyv(taxdt.dds.d.9.com, "OTU")
setkeyv(resdt.dds.d.9.narrow.shed, "OTU")
resdt.dds.d.9.narrow.shed <- taxdt.dds.d.9.com[resdt.dds.d.9.narrow.shed]
resdt.dds.d.9.narrow.shed## OTU
## 1: ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 2: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
## 3: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
## 4: ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 5: ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
## ---
## 1586: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
## Kingdom Phylum Class Order
## 1: Bacteria Firmicutes Clostridia Clostridiales
## 2: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 3: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 4: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 5: Bacteria Firmicutes Clostridia Clostridiales
## ---
## 1586: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1587: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1588: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1589: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1590: Archaea Euryarchaeota Methanobacteria Methanobacteriales
## Family Genus Species baseMean
## 1: Ruminococcaceae NA NA 0.000000
## 2: Fusobacteriaceae Fusobacterium nucleatum 0.000000
## 3: Fusobacteriaceae Fusobacterium NA 0.000000
## 4: Rikenellaceae NA NA 0.000000
## 5: Eubacteriaceae Eubacterium NA 0.000000
## ---
## 1586: Bacteroidaceae Bacteroides stercoris 58.270669
## 1587: Bacteroidaceae Bacteroides NA 52.257748
## 1588: Prevotellaceae Prevotella NA 0.000000
## 1589: Prevotellaceae Prevotella bivia 0.000000
## 1590: Methanobacteriaceae Methanobrevibacter NA 4.821277
## log2FoldChange lfcSE stat pvalue padj
## 1: NA NA NA NA NA
## 2: NA NA NA NA NA
## 3: NA NA NA NA NA
## 4: NA NA NA NA NA
## 5: NA NA NA NA NA
## ---
## 1586: -22.64520 3.534361 -6.4071542 1.482609e-10 1.980765e-09
## 1587: -22.49760 3.534424 -6.3652800 1.949338e-10 2.325282e-09
## 1588: NA NA NA NA NA
## 1589: NA NA NA NA NA
## 1590: -2.77656 3.465376 -0.8012292 4.229990e-01 6.825201e-01resdt.dds.d.9.narrow.shed[, Significant := padj < alpha]
resdt.dds.d.9.narrow.shed[!is.na(Significant)]## OTU
## 1: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 2: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGTAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 3: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTTAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 4: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 5: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## ---
## 330: TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCGGTTTCGTAAGTCGTGTGTGAAAGGCGGGGGCTCAACCCCCGGACTGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG
## 331: TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG
## 332: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 333: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 334: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
## Kingdom Phylum Class Order
## 1: Bacteria Firmicutes Clostridia Clostridiales
## 2: Bacteria Firmicutes Clostridia Clostridiales
## 3: Bacteria Firmicutes Clostridia Clostridiales
## 4: Bacteria Firmicutes Clostridia Clostridiales
## 5: Bacteria Firmicutes Clostridia Clostridiales
## ---
## 330: Bacteria Verrucomicrobia Verrucomicrobiae Verrucomicrobiales
## 331: Bacteria Verrucomicrobia Verrucomicrobiae Verrucomicrobiales
## 332: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 333: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 334: Archaea Euryarchaeota Methanobacteria Methanobacteriales
## Family Genus Species baseMean
## 1: Ruminococcaceae Faecalibacterium prausnitzii 2195.621485
## 2: Ruminococcaceae Faecalibacterium NA 28.411359
## 3: Ruminococcaceae Faecalibacterium NA 46.137588
## 4: Ruminococcaceae Faecalibacterium prausnitzii 1704.807731
## 5: Ruminococcaceae Faecalibacterium NA 4.517713
## ---
## 330: Verrucomicrobiaceae Akkermansia NA 23.562976
## 331: Verrucomicrobiaceae Akkermansia muciniphila 27.933233
## 332: Bacteroidaceae Bacteroides stercoris 58.270669
## 333: Bacteroidaceae Bacteroides NA 52.257748
## 334: Methanobacteriaceae Methanobrevibacter NA 4.821277
## log2FoldChange lfcSE stat pvalue padj
## 1: 0.5439154 1.705522 0.3189143 7.497915e-01 9.089230e-01
## 2: 22.9451456 3.456224 6.6387907 3.162671e-11 7.042214e-10
## 3: -0.5440902 3.336748 -0.1630600 8.704712e-01 9.635057e-01
## 4: 0.3760386 1.508691 0.2492482 8.031688e-01 9.200151e-01
## 5: -4.8752594 3.540803 -1.3768794 1.685495e-01 3.525053e-01
## ---
## 330: -21.4181238 3.535161 -6.0585990 1.373122e-09 9.970060e-09
## 331: 0.3623402 3.338275 0.1085411 9.135664e-01 9.758427e-01
## 332: -22.6451975 3.534361 -6.4071542 1.482609e-10 1.980765e-09
## 333: -22.4975970 3.534424 -6.3652800 1.949338e-10 2.325282e-09
## 334: -2.7765605 3.465376 -0.8012292 4.229990e-01 6.825201e-01
## Significant
## 1: FALSE
## 2: TRUE
## 3: FALSE
## 4: FALSE
## 5: FALSE
## ---
## 330: TRUE
## 331: FALSE
## 332: TRUE
## 333: TRUE
## 334: FALSEresdt.dds.d.9.narrow.shed## OTU
## 1: ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 2: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
## 3: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
## 4: ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 5: ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
## ---
## 1586: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
## Kingdom Phylum Class Order
## 1: Bacteria Firmicutes Clostridia Clostridiales
## 2: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 3: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 4: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 5: Bacteria Firmicutes Clostridia Clostridiales
## ---
## 1586: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1587: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1588: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1589: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1590: Archaea Euryarchaeota Methanobacteria Methanobacteriales
## Family Genus Species baseMean
## 1: Ruminococcaceae NA NA 0.000000
## 2: Fusobacteriaceae Fusobacterium nucleatum 0.000000
## 3: Fusobacteriaceae Fusobacterium NA 0.000000
## 4: Rikenellaceae NA NA 0.000000
## 5: Eubacteriaceae Eubacterium NA 0.000000
## ---
## 1586: Bacteroidaceae Bacteroides stercoris 58.270669
## 1587: Bacteroidaceae Bacteroides NA 52.257748
## 1588: Prevotellaceae Prevotella NA 0.000000
## 1589: Prevotellaceae Prevotella bivia 0.000000
## 1590: Methanobacteriaceae Methanobrevibacter NA 4.821277
## log2FoldChange lfcSE stat pvalue padj
## 1: NA NA NA NA NA
## 2: NA NA NA NA NA
## 3: NA NA NA NA NA
## 4: NA NA NA NA NA
## 5: NA NA NA NA NA
## ---
## 1586: -22.64520 3.534361 -6.4071542 1.482609e-10 1.980765e-09
## 1587: -22.49760 3.534424 -6.3652800 1.949338e-10 2.325282e-09
## 1588: NA NA NA NA NA
## 1589: NA NA NA NA NA
## 1590: -2.77656 3.465376 -0.8012292 4.229990e-01 6.825201e-01
## Significant
## 1: NA
## 2: NA
## 3: NA
## 4: NA
## 5: NA
## ---
## 1586: TRUE
## 1587: TRUE
## 1588: NA
## 1589: NA
## 1590: FALSEvolcano.d.9.narrow.shed = ggplot(
data = resdt.dds.d.9.narrow.shed[!is.na(Significant)][(pvalue < 1)],
mapping = aes(x = log2FoldChange,
y = -log10(pvalue),
color = Phylum,
label = OTU, label1 = Genus)) +
theme_bw() +
geom_point() +
geom_point(data = resdt.dds.d.9.narrow.shed[(Significant)], size = 7, alpha = 0.7) +
# geom_text(data = resdt[(Significant)], mapping = aes(label = paste("Genus:", Genus)), color = "black", size = 3) +
theme(axis.text.x = element_text(angle = -90, hjust = 0, vjust=0.5)) +
geom_hline(yintercept = -log10(alpha)) +
ggtitle("DESeq2 Negative Binomial Test Volcano Plot\nDay -9 Narrow Spectrum Antibiotics ~ Shedding") +
theme(axis.title = element_text(size=12)) +
theme(axis.text = element_text(size=12)) +
theme(legend.text = element_text(size=12)) +
geom_vline(xintercept = 0, lty = 2)
volcano.d.9.narrow.shed
summary(res.dds.d.9.narrow.shed)##
## out of 469 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up) : 24, 5.1%
## LFC < 0 (down) : 70, 15%
## outliers [1] : 0, 0%
## low counts [2] : 135, 29%
## (mean count < 3)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?resultsmcols(res.dds.d.9.narrow.shed, use.names = TRUE)## DataFrame with 6 rows and 2 columns
## type
## <character>
## baseMean intermediate
## log2FoldChange results
## lfcSE results
## stat results
## pvalue results
## padj results
## description
## <character>
## baseMean mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): Shedding Shedding vs No.shedding
## lfcSE standard error: Shedding Shedding vs No.shedding
## stat Wald statistic: Shedding Shedding vs No.shedding
## pvalue Wald test p-value: Shedding Shedding vs No.shedding
## padj BH adjusted p-valuesggplotly(volcano.d.9.narrow.shed)Shedding: Day -9 Broad Spectrum Antibiotics
sample_data(ps1)$day## [1] -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9
## [24] -9 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7
## [47] 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 0 0 0
## [70] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## [93] 0 0 0 0 0 0 0 0ps1.d.9.broad <- subset_samples(ps1.broad, day == "-9")
sample_data(ps1.d.9.broad)$day## [1] -9 -9 -9 -9 -9 -9 -9
## Levels: -9sample_data(ps1.d.9.broad)$randomization_arm## [1] Broad spectrum antibiotics Broad spectrum antibiotics
## [3] Broad spectrum antibiotics Broad spectrum antibiotics
## [5] Broad spectrum antibiotics Broad spectrum antibiotics
## [7] Broad spectrum antibiotics
## Levels: Broad spectrum antibiotics# Differential Abundance Testing
ds.d.9.broad <- phyloseq_to_deseq2(ps1.d.9.broad, ~Shedding)
geoMeans.ds.d.9.broad <- apply(counts(ds.d.9.broad), 1, gm_mean)
ds.d.9.broad <- estimateSizeFactors(ds.d.9.broad, geoMeans = geoMeans.ds.d.9.broad)
dds.d.9.broad <- DESeq(ds.d.9.broad, test="Wald", fitType="local", betaPrior = FALSE)
alpha = 0.05
# Tabulate and write results
res.dds.d.9.broad = results(dds.d.9.broad, cooksCutoff = FALSE)
sigtab_dds.dds.d.9.broad = res.dds.d.9.broad[which(res.dds.d.9.broad$padj < alpha), ]
sigtab_dds.dds.d.9.broad = cbind(as(sigtab_dds.dds.d.9.broad, "data.frame"), as(tax_table(ps1.d.9.broad)[rownames(sigtab_dds.dds.d.9.broad), ], "matrix"))
summary(res.dds.d.9.broad)##
## out of 464 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up) : 1, 0.22%
## LFC < 0 (down) : 76, 16%
## outliers [1] : 0, 0%
## low counts [2] : 0, 0%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?resultshead(sigtab_dds.dds.d.9.broad)## baseMean
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 358.3718
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 1143.4846
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 263.9524
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 613.9829
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAAACTGCATTTGAAACTGTAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 136.5218
## GCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGATAGCAAGTCAGCTGTGAAAACTATGGGCTCAACCCATAAACTGCAGTTGAAACTGTTATTCTTGAGTGGAGTAGAGGCAAGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGGCTCTAACTGACGCTGAGGCTCGAAAGTGTGGGG 124.0001
## log2FoldChange
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT -11.077215
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT -25.168109
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG -21.221568
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT -24.209249
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAAACTGCATTTGAAACTGTAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT -9.684908
## GCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGATAGCAAGTCAGCTGTGAAAACTATGGGCTCAACCCATAAACTGCAGTTGAAACTGTTATTCTTGAGTGGAGTAGAGGCAAGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGGCTCTAACTGACGCTGAGGCTCGAAAGTGTGGGG -21.848371
## lfcSE
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 3.475980
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 5.333306
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 5.333438
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 5.333340
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAAACTGCATTTGAAACTGTAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 3.477524
## GCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGATAGCAAGTCAGCTGTGAAAACTATGGGCTCAACCCATAAACTGCAGTTGAAACTGTTATTCTTGAGTGGAGTAGAGGCAAGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGGCTCTAACTGACGCTGAGGCTCGAAAGTGTGGGG 5.333631
## stat
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT -3.186789
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT -4.719044
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG -3.978966
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT -4.539228
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAAACTGCATTTGAAACTGTAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT -2.785001
## GCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGATAGCAAGTCAGCTGTGAAAACTATGGGCTCAACCCATAAACTGCAGTTGAAACTGTTATTCTTGAGTGGAGTAGAGGCAAGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGGCTCTAACTGACGCTGAGGCTCGAAAGTGTGGGG -4.096341
## pvalue
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 1.438616e-03
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 2.369551e-06
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 6.921561e-05
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 5.646051e-06
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAAACTGCATTTGAAACTGTAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 5.352757e-03
## GCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGATAGCAAGTCAGCTGTGAAAACTATGGGCTCAACCCATAAACTGCAGTTGAAACTGTTATTCTTGAGTGGAGTAGAGGCAAGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGGCTCTAACTGACGCTGAGGCTCGAAAGTGTGGGG 4.197310e-05
## padj
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 0.009816442
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 0.001099472
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 0.002316514
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 0.001309884
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAAACTGCATTTGAAACTGTAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 0.034981398
## GCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGATAGCAAGTCAGCTGTGAAAACTATGGGCTCAACCCATAAACTGCAGTTGAAACTGTTATTCTTGAGTGGAGTAGAGGCAAGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGGCTCTAACTGACGCTGAGGCTCGAAAGTGTGGGG 0.001989000
## Kingdom
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteria
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteria
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Bacteria
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Bacteria
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAAACTGCATTTGAAACTGTAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT Bacteria
## GCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGATAGCAAGTCAGCTGTGAAAACTATGGGCTCAACCCATAAACTGCAGTTGAAACTGTTATTCTTGAGTGGAGTAGAGGCAAGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGGCTCTAACTGACGCTGAGGCTCGAAAGTGTGGGG Bacteria
## Phylum
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroidetes
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidetes
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Firmicutes
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Firmicutes
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAAACTGCATTTGAAACTGTAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT Firmicutes
## GCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGATAGCAAGTCAGCTGTGAAAACTATGGGCTCAACCCATAAACTGCAGTTGAAACTGTTATTCTTGAGTGGAGTAGAGGCAAGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGGCTCTAACTGACGCTGAGGCTCGAAAGTGTGGGG Firmicutes
## Class
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroidia
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidia
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Negativicutes
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Clostridia
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAAACTGCATTTGAAACTGTAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT Clostridia
## GCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGATAGCAAGTCAGCTGTGAAAACTATGGGCTCAACCCATAAACTGCAGTTGAAACTGTTATTCTTGAGTGGAGTAGAGGCAAGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGGCTCTAACTGACGCTGAGGCTCGAAAGTGTGGGG Clostridia
## Order
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroidales
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidales
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Selenomonadales
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Clostridiales
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAAACTGCATTTGAAACTGTAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT Clostridiales
## GCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGATAGCAAGTCAGCTGTGAAAACTATGGGCTCAACCCATAAACTGCAGTTGAAACTGTTATTCTTGAGTGGAGTAGAGGCAAGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGGCTCTAACTGACGCTGAGGCTCGAAAGTGTGGGG Clostridiales
## Family
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroidaceae
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Prevotellaceae
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Veillonellaceae
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Ruminococcaceae
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAAACTGCATTTGAAACTGTAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT Ruminococcaceae
## GCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGATAGCAAGTCAGCTGTGAAAACTATGGGCTCAACCCATAAACTGCAGTTGAAACTGTTATTCTTGAGTGGAGTAGAGGCAAGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGGCTCTAACTGACGCTGAGGCTCGAAAGTGTGGGG Ruminococcaceae
## Genus
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroides
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Prevotella
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Dialister
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Faecalibacterium
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAAACTGCATTTGAAACTGTAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT Ruminococcus
## GCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGATAGCAAGTCAGCTGTGAAAACTATGGGCTCAACCCATAAACTGCAGTTGAAACTGTTATTCTTGAGTGGAGTAGAGGCAAGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGGCTCTAACTGACGCTGAGGCTCGAAAGTGTGGGG <NA>
## Species
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT <NA>
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT <NA>
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG <NA>
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT prausnitzii
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAAACTGCATTTGAAACTGTAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT bromii
## GCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGATAGCAAGTCAGCTGTGAAAACTATGGGCTCAACCCATAAACTGCAGTTGAAACTGTTATTCTTGAGTGGAGTAGAGGCAAGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGGCTCTAACTGACGCTGAGGCTCGAAAGTGTGGGG <NA>write.table(sigtab_dds.dds.d.9.broad, file="./results/deseq_d.9_broad_Shedding.txt", sep = "\t") # Change filename to save results to appropriate file
# Quick check of factor levels
mcols(res.dds.d.9.broad, use.names = TRUE)## DataFrame with 6 rows and 2 columns
## type
## <character>
## baseMean intermediate
## log2FoldChange results
## lfcSE results
## stat results
## pvalue results
## padj results
## description
## <character>
## baseMean mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): Shedding Shedding vs No.shedding
## lfcSE standard error: Shedding Shedding vs No.shedding
## stat Wald statistic: Shedding Shedding vs No.shedding
## pvalue Wald test p-value: Shedding Shedding vs No.shedding
## padj BH adjusted p-values# Prepare to join results data.table and taxonomy table
resdt.dds.d.9.broad = data.table(as(results(dds.d.9.broad, cooksCutoff = FALSE), "data.frame"),
keep.rownames = TRUE)
setnames(resdt.dds.d.9.broad, "rn", "OTU")
taxdt.dds.d.9.com = data.table(data.frame(as(tax_table(ps1.d.9.broad), "matrix")), keep.rownames = TRUE)
setnames(taxdt.dds.d.9.com, "rn", "OTU")
# Join results data.table and taxonomy table
setkeyv(taxdt.dds.d.9.com, "OTU")
setkeyv(resdt.dds.d.9.broad, "OTU")
resdt.dds.d.9.broad <- taxdt.dds.d.9.com[resdt.dds.d.9.broad]
resdt.dds.d.9.broad## OTU
## 1: ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 2: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
## 3: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
## 4: ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 5: ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
## ---
## 1586: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
## Kingdom Phylum Class Order
## 1: Bacteria Firmicutes Clostridia Clostridiales
## 2: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 3: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 4: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 5: Bacteria Firmicutes Clostridia Clostridiales
## ---
## 1586: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1587: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1588: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1589: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1590: Archaea Euryarchaeota Methanobacteria Methanobacteriales
## Family Genus Species baseMean
## 1: Ruminococcaceae NA NA 0.00000
## 2: Fusobacteriaceae Fusobacterium nucleatum 0.00000
## 3: Fusobacteriaceae Fusobacterium NA 0.00000
## 4: Rikenellaceae NA NA 0.00000
## 5: Eubacteriaceae Eubacterium NA 0.00000
## ---
## 1586: Bacteroidaceae Bacteroides stercoris 0.00000
## 1587: Bacteroidaceae Bacteroides NA 0.00000
## 1588: Prevotellaceae Prevotella NA 0.00000
## 1589: Prevotellaceae Prevotella bivia 0.00000
## 1590: Methanobacteriaceae Methanobrevibacter NA 2.02012
## log2FoldChange lfcSE stat pvalue padj
## 1: NA NA NA NA NA
## 2: NA NA NA NA NA
## 3: NA NA NA NA NA
## 4: NA NA NA NA NA
## 5: NA NA NA NA NA
## ---
## 1586: NA NA NA NA NA
## 1587: NA NA NA NA NA
## 1588: NA NA NA NA NA
## 1589: NA NA NA NA NA
## 1590: -3.688854 5.350637 -0.6894234 0.4905569 0.8381624resdt.dds.d.9.broad[, Significant := padj < alpha]
resdt.dds.d.9.broad[!is.na(Significant)]## OTU
## 1: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTCGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 2: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGCTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 3: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCAGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 4: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 5: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAGCTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## ---
## 460: TCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTGATAAGTTAGAGGTGAAATGTTAGGGCTCAACCCTGAAACTGCCTCTAATACTGTTGGACTAGAGAGTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCTTAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTATATCTGACGTTGAGGCACGAAAGCGTGGGG
## 461: TCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTGATAAGTTAGAGGTGAAATTTCGGGGCTCAACCCTGAACGTGCCTCTAATACTGTTGAGCTAGAGAGTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCTTAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTATATCTGACGTTGAGGCACGAAAGCGTGGGG
## 462: TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCAGGGGCTCAACCCCTGGATTGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG
## 463: TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG
## 464: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
## Kingdom Phylum Class Order
## 1: Bacteria Firmicutes Clostridia Clostridiales
## 2: Bacteria Firmicutes Clostridia Clostridiales
## 3: Bacteria Firmicutes Clostridia Clostridiales
## 4: Bacteria Firmicutes Clostridia Clostridiales
## 5: Bacteria Firmicutes Clostridia Clostridiales
## ---
## 460: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 461: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 462: Bacteria Verrucomicrobia Verrucomicrobiae Verrucomicrobiales
## 463: Bacteria Verrucomicrobia Verrucomicrobiae Verrucomicrobiales
## 464: Archaea Euryarchaeota Methanobacteria Methanobacteriales
## Family Genus Species baseMean
## 1: Ruminococcaceae Faecalibacterium NA 6.867618
## 2: Ruminococcaceae Faecalibacterium NA 254.644237
## 3: Ruminococcaceae Faecalibacterium NA 53.497773
## 4: Ruminococcaceae Faecalibacterium prausnitzii 1720.798723
## 5: Ruminococcaceae Faecalibacterium NA 21.346966
## ---
## 460: Rikenellaceae Alistipes NA 1.716905
## 461: Rikenellaceae Alistipes putredinis 317.759626
## 462: Verrucomicrobiaceae Akkermansia NA 109.357806
## 463: Verrucomicrobiaceae Akkermansia muciniphila 81.646341
## 464: Methanobacteriaceae Methanobrevibacter NA 2.020120
## log2FoldChange lfcSE stat pvalue padj
## 1: -5.3882408 5.339579 -1.0091134 3.129202e-01 0.838162439
## 2: 6.1745647 4.930232 1.2523882 2.104284e-01 0.806932161
## 3: 11.0034829 3.561049 3.0899556 2.001864e-03 0.013461809
## 4: 1.8541965 1.551995 1.1947179 2.321973e-01 0.835190115
## 5: -19.6078629 5.335357 -3.6750801 2.377748e-04 0.002839852
## ---
## 460: -3.4876899 5.351838 -0.6516807 5.146072e-01 0.838162439
## 461: -0.9567253 2.675959 -0.3575261 7.206980e-01 0.860704433
## 462: -21.8225414 5.333679 -4.0914612 4.286638e-05 0.001989000
## 463: -0.5092594 4.931990 -0.1032564 9.177595e-01 0.952663104
## 464: -3.6888541 5.350637 -0.6894234 4.905569e-01 0.838162439
## Significant
## 1: FALSE
## 2: FALSE
## 3: TRUE
## 4: FALSE
## 5: TRUE
## ---
## 460: FALSE
## 461: FALSE
## 462: TRUE
## 463: FALSE
## 464: FALSEresdt.dds.d.9.broad## OTU
## 1: ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 2: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
## 3: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
## 4: ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 5: ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
## ---
## 1586: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
## Kingdom Phylum Class Order
## 1: Bacteria Firmicutes Clostridia Clostridiales
## 2: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 3: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 4: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 5: Bacteria Firmicutes Clostridia Clostridiales
## ---
## 1586: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1587: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1588: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1589: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1590: Archaea Euryarchaeota Methanobacteria Methanobacteriales
## Family Genus Species baseMean
## 1: Ruminococcaceae NA NA 0.00000
## 2: Fusobacteriaceae Fusobacterium nucleatum 0.00000
## 3: Fusobacteriaceae Fusobacterium NA 0.00000
## 4: Rikenellaceae NA NA 0.00000
## 5: Eubacteriaceae Eubacterium NA 0.00000
## ---
## 1586: Bacteroidaceae Bacteroides stercoris 0.00000
## 1587: Bacteroidaceae Bacteroides NA 0.00000
## 1588: Prevotellaceae Prevotella NA 0.00000
## 1589: Prevotellaceae Prevotella bivia 0.00000
## 1590: Methanobacteriaceae Methanobrevibacter NA 2.02012
## log2FoldChange lfcSE stat pvalue padj Significant
## 1: NA NA NA NA NA NA
## 2: NA NA NA NA NA NA
## 3: NA NA NA NA NA NA
## 4: NA NA NA NA NA NA
## 5: NA NA NA NA NA NA
## ---
## 1586: NA NA NA NA NA NA
## 1587: NA NA NA NA NA NA
## 1588: NA NA NA NA NA NA
## 1589: NA NA NA NA NA NA
## 1590: -3.688854 5.350637 -0.6894234 0.4905569 0.8381624 FALSEvolcano.d.9.broad.shed = ggplot(
data = resdt.dds.d.9.broad[!is.na(Significant)][(pvalue < 1)],
mapping = aes(x = log2FoldChange,
y = -log10(pvalue),
color = Phylum,
label = OTU, label1 = Genus)) +
theme_bw() +
geom_point() +
geom_point(data = resdt.dds.d.9.broad[(Significant)], size = 7, alpha = 0.7) +
# geom_text(data = resdt[(Significant)], mapping = aes(label = paste("Genus:", Genus)), color = "black", size = 3) +
theme(axis.text.x = element_text(angle = -90, hjust = 0, vjust=0.5)) +
geom_hline(yintercept = -log10(alpha)) +
ggtitle("DESeq2 Negative Binomial Test Volcano Plot\nDay -9 Broad Spectrum Antibiotics ~ Shedding") +
theme(axis.title = element_text(size=12)) +
theme(axis.text = element_text(size=12)) +
theme(legend.text = element_text(size=12)) +
geom_vline(xintercept = 0, lty = 2)
volcano.d.9.broad.shed
summary(res.dds.d.9.broad)##
## out of 464 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up) : 1, 0.22%
## LFC < 0 (down) : 76, 16%
## outliers [1] : 0, 0%
## low counts [2] : 0, 0%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?resultsmcols(res.dds.d.9.broad, use.names = TRUE)## DataFrame with 6 rows and 2 columns
## type
## <character>
## baseMean intermediate
## log2FoldChange results
## lfcSE results
## stat results
## pvalue results
## padj results
## description
## <character>
## baseMean mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): Shedding Shedding vs No.shedding
## lfcSE standard error: Shedding Shedding vs No.shedding
## stat Wald statistic: Shedding Shedding vs No.shedding
## pvalue Wald test p-value: Shedding Shedding vs No.shedding
## padj BH adjusted p-valuesggplotly(volcano.d.9.broad.shed)Shedding: Day 0 Narrow Spectrum Antibiotics
# Differential Abundance Testing
ds.d0.narrow.shed <- phyloseq_to_deseq2(ps1.d0.narrow, ~Shedding)
geoMeans.ds.d0.narrow.shed <- apply(counts(ds.d0.narrow.shed), 1, gm_mean)
ds.d0.narrow.shed <- estimateSizeFactors(ds.d0.narrow.shed, geoMeans = geoMeans.ds.d0.narrow.shed)
dds.d0.narrow.shed <- DESeq(ds.d0.narrow.shed, test="Wald", fitType="local", betaPrior = FALSE)
alpha = 0.05
# Tabulate and write results
res.dds.d0.narrow.shed = results(dds.d0.narrow.shed, cooksCutoff = FALSE)
sigtab_dds.dds.d0.narrow.shed = res.dds.d0.narrow.shed[which(res.dds.d0.narrow.shed$padj < alpha), ]
sigtab_dds.dds.d0.narrow.shed = cbind(as(sigtab_dds.dds.d0.narrow.shed, "data.frame"), as(tax_table(ps1.d0.narrow)[rownames(sigtab_dds.dds.d0.narrow.shed), ], "matrix"))
summary(res.dds.d0.narrow.shed)##
## out of 141 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up) : 8, 5.7%
## LFC < 0 (down) : 6, 4.3%
## outliers [1] : 0, 0%
## low counts [2] : 99, 70%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?resultshead(sigtab_dds.dds.d0.narrow.shed)## baseMean
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 156.59134
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT 139.68413
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC 915.37064
## GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGAAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT 24.77274
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTTTCATAAGTCTGTCTTAAAAGTGCGGGGCTTAACCCCGTGAGGGGATGGAAACTATGGAACTGGAGTATCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCCAGGGG 28.90231
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGTTTTTTAAGTCTGGAGTGAAAATGCGGGGCTCAACCCCGTATGGCTCTGGATACTGGAAGACTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT 28.85293
## log2FoldChange
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT -24.313898
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT -24.169993
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC 28.834345
## GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGAAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT -21.814995
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTTTCATAAGTCTGTCTTAAAAGTGCGGGGCTTAACCCCGTGAGGGGATGGAAACTATGGAACTGGAGTATCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCCAGGGG -22.030192
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGTTTTTTAAGTCTGGAGTGAAAATGCGGGGCTCAACCCCGTATGGCTCTGGATACTGGAAGACTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT 8.770506
## lfcSE
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 3.102730
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT 3.102746
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC 3.051926
## GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGAAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT 3.103426
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTTTCATAAGTCTGTCTTAAAAGTGCGGGGCTTAACCCCGTGAGGGGATGGAAACTATGGAACTGGAGTATCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCCAGGGG 3.103310
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGTTTTTTAAGTCTGGAGTGAAAATGCGGGGCTCAACCCCGTATGGCTCTGGATACTGGAAGACTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT 3.050965
## stat
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT -7.836291
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT -7.789871
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC 9.447917
## GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGAAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT -7.029327
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTTTCATAAGTCTGTCTTAAAAGTGCGGGGCTTAACCCCGTGAGGGGATGGAAACTATGGAACTGGAGTATCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCCAGGGG -7.098935
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGTTTTTTAAGTCTGGAGTGAAAATGCGGGGCTCAACCCCGTATGGCTCTGGATACTGGAAGACTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT 2.874666
## pvalue
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 4.640501e-15
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT 6.707756e-15
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC 3.456413e-21
## GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGAAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT 2.075325e-12
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTTTCATAAGTCTGTCTTAAAAGTGCGGGGCTTAACCCCGTGAGGGGATGGAAACTATGGAACTGGAGTATCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCCAGGGG 1.257222e-12
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGTTTTTTAAGTCTGGAGTGAAAATGCGGGGCTCAACCCCGTATGGCTCTGGATACTGGAAGACTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT 4.044555e-03
## padj
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 2.996131e-13
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT 2.996131e-13
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC 4.631594e-19
## GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGAAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT 2.780936e-11
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTTTCATAAGTCTGTCTTAAAAGTGCGGGGCTTAACCCCGTGAGGGGATGGAAACTATGGAACTGGAGTATCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCCAGGGG 1.871864e-11
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGTTTTTTAAGTCTGGAGTGAAAATGCGGGGCTCAACCCCGTATGGCTCTGGATACTGGAAGACTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT 4.169003e-02
## Kingdom
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteria
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT Bacteria
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC Bacteria
## GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGAAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT Bacteria
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTTTCATAAGTCTGTCTTAAAAGTGCGGGGCTTAACCCCGTGAGGGGATGGAAACTATGGAACTGGAGTATCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCCAGGGG Bacteria
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGTTTTTTAAGTCTGGAGTGAAAATGCGGGGCTCAACCCCGTATGGCTCTGGATACTGGAAGACTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT Bacteria
## Phylum
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidetes
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT Firmicutes
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC Synergistetes
## GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGAAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT Firmicutes
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTTTCATAAGTCTGTCTTAAAAGTGCGGGGCTTAACCCCGTGAGGGGATGGAAACTATGGAACTGGAGTATCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCCAGGGG Firmicutes
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGTTTTTTAAGTCTGGAGTGAAAATGCGGGGCTCAACCCCGTATGGCTCTGGATACTGGAAGACTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT Firmicutes
## Class
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidia
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT Negativicutes
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC Synergistia
## GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGAAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT Bacilli
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTTTCATAAGTCTGTCTTAAAAGTGCGGGGCTTAACCCCGTGAGGGGATGGAAACTATGGAACTGGAGTATCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCCAGGGG Negativicutes
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGTTTTTTAAGTCTGGAGTGAAAATGCGGGGCTCAACCCCGTATGGCTCTGGATACTGGAAGACTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT Negativicutes
## Order
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidales
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT Selenomonadales
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC Synergistales
## GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGAAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT Lactobacillales
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTTTCATAAGTCTGTCTTAAAAGTGCGGGGCTTAACCCCGTGAGGGGATGGAAACTATGGAACTGGAGTATCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCCAGGGG Selenomonadales
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGTTTTTTAAGTCTGGAGTGAAAATGCGGGGCTCAACCCCGTATGGCTCTGGATACTGGAAGACTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT Selenomonadales
## Family
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Prevotellaceae
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT Acidaminococcaceae
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC Synergistaceae
## GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGAAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT Lactobacillaceae
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTTTCATAAGTCTGTCTTAAAAGTGCGGGGCTTAACCCCGTGAGGGGATGGAAACTATGGAACTGGAGTATCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCCAGGGG Veillonellaceae
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGTTTTTTAAGTCTGGAGTGAAAATGCGGGGCTCAACCCCGTATGGCTCTGGATACTGGAAGACTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT Acidaminococcaceae
## Genus
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Prevotella
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT Acidaminococcus
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC Cloacibacillus
## GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGAAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT Lactobacillus
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTTTCATAAGTCTGTCTTAAAAGTGCGGGGCTTAACCCCGTGAGGGGATGGAAACTATGGAACTGGAGTATCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCCAGGGG Veillonella
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGTTTTTTAAGTCTGGAGTGAAAATGCGGGGCTCAACCCCGTATGGCTCTGGATACTGGAAGACTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT Phascolarctobacterium
## Species
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT copri
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT <NA>
## GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC evryensis
## GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGAAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT ruminis
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTTTCATAAGTCTGTCTTAAAAGTGCGGGGCTTAACCCCGTGAGGGGATGGAAACTATGGAACTGGAGTATCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCCAGGGG <NA>
## GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGTTTTTTAAGTCTGGAGTGAAAATGCGGGGCTCAACCCCGTATGGCTCTGGATACTGGAAGACTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT succinatutenswrite.table(sigtab_dds.dds.d0.narrow.shed, file="./results/deseq_d0_narrow_Shedding.txt", sep = "\t") # Change filename to save results to appropriate file
# Quick check of factor levels
mcols(res.dds.d0.narrow.shed, use.names = TRUE)## DataFrame with 6 rows and 2 columns
## type
## <character>
## baseMean intermediate
## log2FoldChange results
## lfcSE results
## stat results
## pvalue results
## padj results
## description
## <character>
## baseMean mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): Shedding Shedding vs No.shedding
## lfcSE standard error: Shedding Shedding vs No.shedding
## stat Wald statistic: Shedding Shedding vs No.shedding
## pvalue Wald test p-value: Shedding Shedding vs No.shedding
## padj BH adjusted p-values# Prepare to join results data.table and taxonomy table
resdt.dds.d0.narrow.shed = data.table(as(results(dds.d0.narrow.shed, cooksCutoff = FALSE), "data.frame"),
keep.rownames = TRUE)
setnames(resdt.dds.d0.narrow.shed, "rn", "OTU")
taxdt.dds.d0.com = data.table(data.frame(as(tax_table(ps1.d0.narrow), "matrix")), keep.rownames = TRUE)
setnames(taxdt.dds.d0.com, "rn", "OTU")
# Join results data.table and taxonomy table
setkeyv(taxdt.dds.d0.com, "OTU")
setkeyv(resdt.dds.d0.narrow.shed, "OTU")
resdt.dds.d0.narrow.shed <- taxdt.dds.d0.com[resdt.dds.d0.narrow.shed]
resdt.dds.d0.narrow.shed## OTU
## 1: ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 2: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
## 3: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
## 4: ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 5: ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
## ---
## 1586: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
## Kingdom Phylum Class Order
## 1: Bacteria Firmicutes Clostridia Clostridiales
## 2: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 3: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 4: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 5: Bacteria Firmicutes Clostridia Clostridiales
## ---
## 1586: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1587: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1588: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1589: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1590: Archaea Euryarchaeota Methanobacteria Methanobacteriales
## Family Genus Species baseMean
## 1: Ruminococcaceae NA NA 0.0000000
## 2: Fusobacteriaceae Fusobacterium nucleatum 0.0000000
## 3: Fusobacteriaceae Fusobacterium NA 0.3496783
## 4: Rikenellaceae NA NA 0.0000000
## 5: Eubacteriaceae Eubacterium NA 0.0000000
## ---
## 1586: Bacteroidaceae Bacteroides stercoris 0.0000000
## 1587: Bacteroidaceae Bacteroides NA 0.0000000
## 1588: Prevotellaceae Prevotella NA 0.0000000
## 1589: Prevotellaceae Prevotella bivia 0.7704382
## 1590: Methanobacteriaceae Methanobrevibacter NA 7.1099698
## log2FoldChange lfcSE stat pvalue padj
## 1: NA NA NA NA NA
## 2: NA NA NA NA NA
## 3: -0.8529424 3.153197 -0.2705008 0.7867750 0.9486504
## 4: NA NA NA NA NA
## 5: NA NA NA NA NA
## ---
## 1586: NA NA NA NA NA
## 1587: NA NA NA NA NA
## 1588: NA NA NA NA NA
## 1589: -1.9021978 3.128970 -0.6079309 0.5432333 0.9486504
## 1590: 2.9627185 2.991595 0.9903473 0.3220044 0.9458676resdt.dds.d0.narrow.shed[, Significant := padj < alpha]
resdt.dds.d0.narrow.shed[!is.na(Significant)]## OTU
## 1: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
## 2: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAGAACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 3: ACAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGCGCGTAGGCGGACTGTCAAGTCAGTCGTGAAATACCGGGGCTTAACCCCGGGGCTGCGATTGAAACTGACAGCCTTGAGTATCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGTGTGGGG
## 4: CCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGACGGTTATTTAAGTCTGAAGTGAAAGCCCTCAGCTCAACTGAGGAATGGCTTTGGAAACTGGATGACTTGAGTGCAGTAGAGGAAAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGTTGAGGCTCGAAAGTGTGGGT
## 5: CCAGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGATTGTTAAGTCAGCGGTTAAAGGGTGTGGCTCAACCATGCATTGCCGTTGAAACTGGCGATCTTGAGTGCAGACAGGGATGCCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATCGCGAAGGCAGGTGTCCGGGCTGCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## ---
## 130: GCTAGCGTTATCCGGATTTACTGGGCGTAAAGGGTGCGTAGGCGGTCTTTTAAGTCAGGAGTGAAAGGCTACGGCTCAACCGTAGTAAGCTCTTGAAACTGGAGGACTTGAGTGCAGGAGAGGAGAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTAGCGAAGGCGGCTCTCTGGACTGTAACTGACGCTGAGGCACGAAAGCGTGGGG
## 131: GCTAGCGTTATCCGGATTTACTGGGCGTAAAGGGTGCGTAGGTGGTTTCTTAAGTCAGGAGTGAAAGGCTACGGCTCAACCGTAGTAAGCTCTTGAAACTGGGAAACTTGAGTGCAGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTAGCGAAGGCGGCTTTCTGGACTGTAACTGACACTGAGGCACGAAAGCGTGGGG
## 132: TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG
## 133: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 134: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
## Kingdom Phylum Class Order
## 1: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 2: Bacteria Firmicutes Clostridia Clostridiales
## 3: Bacteria Firmicutes Clostridia Clostridiales
## 4: Bacteria Firmicutes Bacilli Lactobacillales
## 5: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## ---
## 130: Bacteria Firmicutes Clostridia Clostridiales
## 131: Bacteria Firmicutes Clostridia Clostridiales
## 132: Bacteria Verrucomicrobia Verrucomicrobiae Verrucomicrobiales
## 133: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 134: Archaea Euryarchaeota Methanobacteria Methanobacteriales
## Family Genus Species baseMean
## 1: Fusobacteriaceae Fusobacterium NA 0.3496783
## 2: Ruminococcaceae Faecalibacterium prausnitzii 3.1347101
## 3: Ruminococcaceae NA NA 0.1861645
## 4: Leuconostocaceae Weissella NA 0.5050118
## 5: Prevotellaceae Paraprevotella NA 0.3705344
## ---
## 130: Peptostreptococcaceae Intestinibacter bartlettii 1.0239045
## 131: Peptostreptococcaceae Terrisporobacter NA 1.9173003
## 132: Verrucomicrobiaceae Akkermansia muciniphila 1514.3149871
## 133: Prevotellaceae Prevotella bivia 0.7704382
## 134: Methanobacteriaceae Methanobrevibacter NA 7.1099698
## log2FoldChange lfcSE stat pvalue padj Significant
## 1: -0.8529424 3.153197 -0.2705008 0.78677498 0.9486504 FALSE
## 2: 3.6439035 3.037194 1.1997599 0.23023260 0.7712792 FALSE
## 3: 2.4578628 3.180233 0.7728561 0.43960753 0.9486504 FALSE
## 4: -1.3169564 3.141858 -0.4191649 0.67509563 0.9486504 FALSE
## 5: -0.4681159 3.162862 -0.1480039 0.88233968 0.9486504 FALSE
## ---
## 130: 4.4155072 3.098948 1.4248406 0.15420329 0.6302357 FALSE
## 131: 5.3064398 3.077400 1.7243257 0.08464906 0.4616041 FALSE
## 132: -0.7327842 2.965545 -0.2470994 0.80483132 0.9486504 FALSE
## 133: -1.9021978 3.128970 -0.6079309 0.54323332 0.9486504 FALSE
## 134: 2.9627185 2.991595 0.9903473 0.32200440 0.9458676 FALSEresdt.dds.d0.narrow.shed## OTU
## 1: ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 2: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
## 3: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
## 4: ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 5: ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
## ---
## 1586: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
## Kingdom Phylum Class Order
## 1: Bacteria Firmicutes Clostridia Clostridiales
## 2: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 3: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 4: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 5: Bacteria Firmicutes Clostridia Clostridiales
## ---
## 1586: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1587: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1588: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1589: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1590: Archaea Euryarchaeota Methanobacteria Methanobacteriales
## Family Genus Species baseMean
## 1: Ruminococcaceae NA NA 0.0000000
## 2: Fusobacteriaceae Fusobacterium nucleatum 0.0000000
## 3: Fusobacteriaceae Fusobacterium NA 0.3496783
## 4: Rikenellaceae NA NA 0.0000000
## 5: Eubacteriaceae Eubacterium NA 0.0000000
## ---
## 1586: Bacteroidaceae Bacteroides stercoris 0.0000000
## 1587: Bacteroidaceae Bacteroides NA 0.0000000
## 1588: Prevotellaceae Prevotella NA 0.0000000
## 1589: Prevotellaceae Prevotella bivia 0.7704382
## 1590: Methanobacteriaceae Methanobrevibacter NA 7.1099698
## log2FoldChange lfcSE stat pvalue padj Significant
## 1: NA NA NA NA NA NA
## 2: NA NA NA NA NA NA
## 3: -0.8529424 3.153197 -0.2705008 0.7867750 0.9486504 FALSE
## 4: NA NA NA NA NA NA
## 5: NA NA NA NA NA NA
## ---
## 1586: NA NA NA NA NA NA
## 1587: NA NA NA NA NA NA
## 1588: NA NA NA NA NA NA
## 1589: -1.9021978 3.128970 -0.6079309 0.5432333 0.9486504 FALSE
## 1590: 2.9627185 2.991595 0.9903473 0.3220044 0.9458676 FALSEvolcano.d0.narrow.shed = ggplot(
data = resdt.dds.d0.narrow.shed[!is.na(Significant)][(pvalue < 1)],
mapping = aes(x = log2FoldChange,
y = -log10(pvalue),
color = Phylum,
label = OTU, label1 = Genus)) +
theme_bw() +
geom_point() +
geom_point(data = resdt.dds.d0.narrow.shed[(Significant)], size = 7, alpha = 0.7) +
# geom_text(data = resdt[(Significant)], mapping = aes(label = paste("Genus:", Genus)), color = "black", size = 3) +
theme(axis.text.x = element_text(angle = -90, hjust = 0, vjust=0.5)) +
geom_hline(yintercept = -log10(alpha)) +
ggtitle("DESeq2 Negative Binomial Test Volcano Plot\nDay 0 Narrow Spectrum Antibiotics ~ Shedding") +
theme(axis.title = element_text(size=12)) +
theme(axis.text = element_text(size=12)) +
theme(legend.text = element_text(size=12)) +
geom_vline(xintercept = 0, lty = 2)
volcano.d0.narrow.shed
summary(res.dds.d0.narrow.shed)##
## out of 141 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up) : 8, 5.7%
## LFC < 0 (down) : 6, 4.3%
## outliers [1] : 0, 0%
## low counts [2] : 99, 70%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?resultsmcols(res.dds.d0.narrow.shed, use.names = TRUE)## DataFrame with 6 rows and 2 columns
## type
## <character>
## baseMean intermediate
## log2FoldChange results
## lfcSE results
## stat results
## pvalue results
## padj results
## description
## <character>
## baseMean mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): Shedding Shedding vs No.shedding
## lfcSE standard error: Shedding Shedding vs No.shedding
## stat Wald statistic: Shedding Shedding vs No.shedding
## pvalue Wald test p-value: Shedding Shedding vs No.shedding
## padj BH adjusted p-valuesggplotly(volcano.d0.narrow.shed)Shedding: Day 0 Broad Spectrum Antibiotics
sample_data(ps1)$day## [1] -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9
## [24] -9 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7
## [47] 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 0 0 0
## [70] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## [93] 0 0 0 0 0 0 0 0ps1.d0.broad <- subset_samples(ps1.broad, day == "0")
sample_data(ps1.d0.broad)$day## [1] 0 0 0 0 0 0 0 0 0 0
## Levels: 0sample_data(ps1.d0.broad)$randomization_arm## [1] Broad spectrum antibiotics Broad spectrum antibiotics
## [3] Broad spectrum antibiotics Broad spectrum antibiotics
## [5] Broad spectrum antibiotics Broad spectrum antibiotics
## [7] Broad spectrum antibiotics Broad spectrum antibiotics
## [9] Broad spectrum antibiotics Broad spectrum antibiotics
## Levels: Broad spectrum antibiotics# Differential Abundance Testing
ds.d0.broad <- phyloseq_to_deseq2(ps1.d0.broad, ~Shedding)
geoMeans.ds.d0.broad <- apply(counts(ds.d0.broad), 1, gm_mean)
ds.d0.broad <- estimateSizeFactors(ds.d0.broad, geoMeans = geoMeans.ds.d0.broad)
dds.d0.broad <- DESeq(ds.d0.broad, test="Wald", fitType="local", betaPrior = FALSE)
alpha = 0.05
# Tabulate and write results
res.dds.d0.broad = results(dds.d0.broad, cooksCutoff = FALSE)
sigtab_dds.dds.d0.broad = res.dds.d0.broad[which(res.dds.d0.broad$padj < alpha), ]
sigtab_dds.dds.d0.broad = cbind(as(sigtab_dds.dds.d0.broad, "data.frame"), as(tax_table(ps1.d0.broad)[rownames(sigtab_dds.dds.d0.broad), ], "matrix"))
summary(res.dds.d0.broad)##
## out of 88 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up) : 0, 0%
## LFC < 0 (down) : 1, 1.1%
## outliers [1] : 0, 0%
## low counts [2] : 34, 39%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?resultshead(sigtab_dds.dds.d0.broad)## baseMean
## GCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTCTTTTAAGTCTAATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT 245.1928
## log2FoldChange
## GCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTCTTTTAAGTCTAATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT -23.83235
## lfcSE
## GCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTCTTTTAAGTCTAATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT 3.884625
## stat
## GCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTCTTTTAAGTCTAATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT -6.135045
## pvalue
## GCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTCTTTTAAGTCTAATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT 8.513503e-10
## padj
## GCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTCTTTTAAGTCTAATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT 7.491883e-08
## Kingdom
## GCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTCTTTTAAGTCTAATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT Bacteria
## Phylum
## GCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTCTTTTAAGTCTAATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT Firmicutes
## Class
## GCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTCTTTTAAGTCTAATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT Bacilli
## Order
## GCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTCTTTTAAGTCTAATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT Lactobacillales
## Family
## GCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTCTTTTAAGTCTAATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT Lactobacillaceae
## Genus
## GCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTCTTTTAAGTCTAATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT Pediococcus
## Species
## GCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTCTTTTAAGTCTAATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT <NA>write.table(sigtab_dds.dds.d0.broad, file="./results/deseq_d0_broad_Shedding.txt", sep = "\t") # Change filename to save results to appropriate file
# Quick check of factor levels
mcols(res.dds.d0.broad, use.names = TRUE)## DataFrame with 6 rows and 2 columns
## type
## <character>
## baseMean intermediate
## log2FoldChange results
## lfcSE results
## stat results
## pvalue results
## padj results
## description
## <character>
## baseMean mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): Shedding Shedding vs No.shedding
## lfcSE standard error: Shedding Shedding vs No.shedding
## stat Wald statistic: Shedding Shedding vs No.shedding
## pvalue Wald test p-value: Shedding Shedding vs No.shedding
## padj BH adjusted p-values# Prepare to join results data.table and taxonomy table
resdt.dds.d0.broad = data.table(as(results(dds.d0.broad, cooksCutoff = FALSE), "data.frame"),
keep.rownames = TRUE)
setnames(resdt.dds.d0.broad, "rn", "OTU")
taxdt.dds.d0.com = data.table(data.frame(as(tax_table(ps1.d0.broad), "matrix")), keep.rownames = TRUE)
setnames(taxdt.dds.d0.com, "rn", "OTU")
# Join results data.table and taxonomy table
setkeyv(taxdt.dds.d0.com, "OTU")
setkeyv(resdt.dds.d0.broad, "OTU")
resdt.dds.d0.broad <- taxdt.dds.d0.com[resdt.dds.d0.broad]
resdt.dds.d0.broad## OTU
## 1: ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 2: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
## 3: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
## 4: ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 5: ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
## ---
## 1586: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
## Kingdom Phylum Class Order
## 1: Bacteria Firmicutes Clostridia Clostridiales
## 2: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 3: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 4: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 5: Bacteria Firmicutes Clostridia Clostridiales
## ---
## 1586: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1587: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1588: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1589: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1590: Archaea Euryarchaeota Methanobacteria Methanobacteriales
## Family Genus Species baseMean
## 1: Ruminococcaceae NA NA 0
## 2: Fusobacteriaceae Fusobacterium nucleatum 0
## 3: Fusobacteriaceae Fusobacterium NA 0
## 4: Rikenellaceae NA NA 0
## 5: Eubacteriaceae Eubacterium NA 0
## ---
## 1586: Bacteroidaceae Bacteroides stercoris 0
## 1587: Bacteroidaceae Bacteroides NA 0
## 1588: Prevotellaceae Prevotella NA 0
## 1589: Prevotellaceae Prevotella bivia 0
## 1590: Methanobacteriaceae Methanobrevibacter NA 0
## log2FoldChange lfcSE stat pvalue padj
## 1: NA NA NA NA NA
## 2: NA NA NA NA NA
## 3: NA NA NA NA NA
## 4: NA NA NA NA NA
## 5: NA NA NA NA NA
## ---
## 1586: NA NA NA NA NA
## 1587: NA NA NA NA NA
## 1588: NA NA NA NA NA
## 1589: NA NA NA NA NA
## 1590: NA NA NA NA NAresdt.dds.d0.broad[, Significant := padj < alpha]
resdt.dds.d0.broad[!is.na(Significant)]## OTU
## 1: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 2: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 3: CCAGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGCCCCTTAAGCGTGTTGTGAAATGCCGCGGCTCAACCGTGGCACTGCAGCGCGAACTGGGGGGCTTGAGTGCACGCAACGCAGGTGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTGCGGGAGTGCGACTGACGCTGAAGCTCGAAGGTGCGGGT
## 4: CCGAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGACGGTTCGATAAGTCTGAAGTGAAAGCCCACAGCTCAACTGTGGAATGGCTTTGGAAACTGTCGAACTTGAGTGCAGTAGAGGTAAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTTACTGGACTGCAACTGACGTTGAGGCTCGAAAGTGTGGGT
## 5: CCGAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGACGGTTGATTAAGTCTGATGTGAAAGCCCGGAGCTCAACTCCGGAAAGGCATTGGAAACTGGTCAACTTGAGTGCAGTAGAGGTAAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGCGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGTGTGGGT
## 6: CCGAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTAGATAAGTCTGAAGTTAAAGGCTGTGGCTTAACCATAGTACGCTTTGGAAACTGTTTAACTTGAGTGCAGAAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGG
## 7: CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT
## 8: CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAATTGATACTGGCAGTCTTGAGTACAGTTGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTAACCTGTAACTGACATTGATGCTCGAAAGTGTGGGT
## 9: CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGACAGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCTGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGACTGCAACTGACACTGATGCTCGAAAGTGTGGGT
## 10: CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGT
## 11: CCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTGATAAGTCTGAAGTTAAAGGCTGTGGCTCAACCATAGTTCGCTTTGGAAACTGTCAAACTTGAGTGCAGAAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGG
## 12: CCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGTGGTTTATTAAGTCTGGTGTAAAAGGCAGTGGCTCAACCATTGTATGCATTGGAAACTGGTAGACTTGAGTGCAGGAGAGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGCCTGTAACTGACACTGAGGCTCGAAAGCGTGGGG
## 13: CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 14: CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGATTGCTGGACGATAACTGACGGTGAGGCGCGAAAGTGTGGGG
## 15: CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGAACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 16: CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGTGGCTCAACCTCTGCACTGCAGCGCGAACTGGTCTTCTTGAGTACGCACAACGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACGGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 17: CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTCTTATAAGCGTGTTGTGAAATGTCGGGGCTCAACCTGGGCATTGCAGCGCGAACTGTGAGGCTTGAGTGCGCAGGAAGTAGGCGGAATTCGTCGTGTAGCGGTGAAATGCTTAGATATGACGAAGAACTCCGATTGCGAAGGCAGCCTGCTGTAGCGCAACTGACGCTGAAGCTCGAAAGCGTGGGT
## 18: GCAAGCGTTAATCGGAATCACTGGGCGTAAAGCGCACGTAGGCGGCTTGGTAAGTCAGGGGTGAAATCCCACAGCCCAACTGTGGAACTGCCTTTGATACTGCCAGGCTTGAGTACCGGAGAGGGTGGCGGAATTCCAGGTGTAGGAGTGAAATCCGTAGATATCTGGAGGAACACCGGTGGCGAAGGCGGCCACCTGGACGGTAACTGACGCTGAGGTGCGAAAGCGTGGGT
## 19: GCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGGCAGGCTGGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGTGCGAAAGCGTGGGG
## 20: GCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGG
## 21: GCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTCGCTAAGACAGATGTGAAATCCCCGGGCTTAACCTGGGAACTGCATTTGTGACTGGCGGGCTAGAGTATGGCAGAGGGGGGTAGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAATACCGATGGCGAAGGCAGCCCCCTGGGCCAATACTGACGCTCATGCACGAAAGCGTGGGG
## 22: GCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTTCGTAAGATAGATGTGAAATCCCCGGGCTCAACCTGGGAATTGCATTTATGACTGCGGGACTGGAGTTTGTCAGAGGGGGGTGGAATTCCAAGTGTAGCAGTGAAATGCGTAGATATTTGGAAGAACACCGATGGCGAAGGCAGCCCCCTGGGACATGACTGACGCTCATGCACGAAAGCGTGGGG
## 23: GCAAGCGTTATCCGGAATTATTGGGCGTAAAGAGGGAGCAGGCGGCAGCAAGGGTCTGTGGTGAAAGCCTGAAGCTTAACTTCAGTAAGCCATAGAAACCAGGCAGCTAGAGTGCAGGAGAGGATCGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAGGCGACGATCTGGCCTGCAACTGACGCTCAGTCCCGAAAGCGTGGGG
## 24: GCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTCTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACACTGAGGCGCGAAAGCGTGGGG
## 25: GCAAGCGTTATCCGGAATTATTGGGCGTAAAGGGCTCGTAGGCGGTTCGTCGCGTCCGGTGTGAAAGTCCATCGCTTAACGGTGGATCCGCGCCGGGTACGGGCGGGCTTGAGTGCGGTAGGGGAGACTGGAATTCCCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACACCAATGGCGAAGGCAGGTCTCTGGGCCGTCACTGACGCTGAGGAGCGAAAGCGTGGGG
## 26: GCAAGCGTTATCCGGAATTATTGGGCGTAAAGGGCTCGTAGGCGGTTCGTCGCGTCCGGTGTGAAAGTCCATCGCTTAACGGTGGATCCGCGCCGGGTACGGGCGGGCTTGAGTGCGGTAGGGGAGACTGGAATTCCCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACACCAATGGCGAAGGCAGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGG
## 27: GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGGACTGCAAGTTGGATGTGAAATACCGTGGCTTAACCACGGAACTGCATCCAAAACTGTAGTTCTTGAGTGAAGTAGAGGCAAGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGGCTTTAACTGACGCTGAGGCTCGAAAGTGTGGGG
## 28: GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTGCGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGTCGTACTAGAGTGTCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGATAACTGACGCTGAGGCTCGAAAGCGTGGGG
## 29: GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCAAGGCAAGTCTGAAGTGAAAGCCCGGTGCTTAACGCCGGGACTGCTTTGGAAACTGTTTGGCTGGAGTGCCGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG
## 30: GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCGAAGCAAGTCTGAAGTGAAAGCCCGGGGCTTAACCCCGGGACTGCTTTGGAAACTGTTTTGCTAGAGTGCTGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACAGTAACTGACGTTGAGGCTCGAAAGCGTGGGG
## 31: GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCTGTGCAAGTCTGAAGTGAAAGGCATGGGCTCAACCTGTGGACTGCTTTGGAAACTGTGCAGCTAGAGTGTCGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGG
## 32: GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTAAAGCAAGTCTGAAGTGAAAGCCCGGGGCTCAACCCCGGGACTGCTTTGGAAACTGTTTAACTAGAGTGCTGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACAGTAACTGACGTTGAGGCTCGAAAGCGTGGGG
## 33: GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGTGTAGGTGGCCAGGCAAGTCAGAAGTGAAAGCCCGGGGCTCAACCCCGGGACTGCTTTTGAAACTGCAGGGCTAGAGTGCAGGAGGGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACTGTAACTGACACTGAGGCTCGAAAGCGTGGGG
## 34: GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGTGTAGGTGGCCATGCAAGTCAGAAGTGAAAATCCGGGGCTCAACCCCGGAACTGCTTTTGAAACTGTAAGGCTGGAGTGCAGGAGGGGTGAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTCACTGGACTGTAACTGACACTGAGGCTCGAAAGCGTGGGG
## 35: GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGTGTAGGTGGCTGCGCAAGTCAGGAGTGAAAGCCCGGGGCTCAACCCCGGGACTGCTCTTGAAACTGCGCGGCTTGAGTGCAGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCGGTGGCGAAGGCGGCCTGCTGGACTGTAACTGACACTGAGGCTCGAAAGCGTGGGG
## 36: GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGTGTAGGCGGGATTGCAAGTCAGATGTGAAAACTGGGGGCTCAACCTCCAGCCTGCATTTGAAACTGTAGTTCTTGAGTGCTGGAGAGGCAATCGGAATTCCGTGTGTAGCGGTGAAATGCGTAGATATACGGAGGAACACCAGTGGCGAAGGCGGATTGCTGGACAGTAACTGACGCTGAGGCGCGAAAGCGTGGGG
## 37: GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGTGTAGGTGGGACTACAAGTCAGGTGTGAAAACCAGGGGCTCAACCTCTGGCCTGCATTTGAAACTGTAGTTCTTGAGTGCTGGAGAGGCAATCGGAATTCCGTGTGTAGCGGTGAAATGCGTAGATATACGGAGGAACACCAGTGGCGAAGGCGGATTGCTGGACAGTAACTGACGCTGAGGCGCGAAAGCGTGGGG
## 38: GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGTGCGTAGGTGGCAAGGCAAGTCTGAAGTGAAAATCCGGGGCTCAACCCCGGAACTGCTTTGGAAACTGTTTAGCTGGAGTACAGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGACTTACTGGACTGCTACTGACACTGAGGCACGAAAGCGTGGGG
## 39: GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGTGCGTAGGTGGTGAGACAAGTCTGAAGTGAAAATCCGGGGCTTAACCCCGGAACTGCTTTGGAAACTGCCTGACTAGAGTACAGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGACTTACTGGACTGCTACTGACACTGAGGCACGAAAGCGTGGGG
## 40: GCAAGCGTTATCCGGATTTATTGGGCGTAAAGAGAGTGCAGGCGGTTTTCTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGGAGAAGTGCATCGGAAACTGGATAACTTGAGTGCAGAAGAGGGTAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTACCTGGTCTGCAACTGACGCTGAGACTCGAAAGCATGGGT
## 41: GCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTCTTTTAAGTCTAATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT
## 42: GCAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGACAGCAAGTTGGATGTGAAATACCGAGGCTTAACCACGGAGCTGCATCCAAAACTGTTGTTCTTGAGTGAAGTAGAGGTAGGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCTTTAACTGACGCTGAGGCTCGAAAGTGTGGGG
## 43: GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCATGTAGGCGGGCTTTTAAGTCTGACGTGAAAATGCGGGGCTTAACCCCGTATGGCGTTGGATACTGGAAGTCTTGAGTGCAGGAGAGGAAAGGGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGT
## 44: GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGATCAGTCAGTCTGTCTTAAAAGTTCGGGGCTTAACCCCGTGATGGGATGGAAACTGCTGATCTAGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGACTTTCTGGACGAAAACTGACGCTGAGGCGCGAAAGCCAGGGG
## 45: GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG
## 46: GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTAATAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGTTAAACTTGAGTGCAGGAGAGAAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTTTGGCCTGTAACTGACACTGAGGCGCGAAAGCGTGGGG
## 47: GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGT
## 48: GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCGCGCAGGCGGCGTCGTAAGTCGGTCTTAAAAGTGCGGGGCTTAACCCCGTGAGGGGACCGAAACTGCGATGCTAGAGTATCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAAGCGGCTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCCAGGGG
## 49: GCAAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGCGGATTTTTAAGTGAGATGTGAAATACCCGGGCTTAACTTGGGTGCTGCATTTCAAACTGGAAGTCTAGAGTGCAGGAGAGGAGAAGGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCAGTGGCGAAGGCGCTTCTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGG
## 50: GCAAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGTGGATATTTAAGTGGGATGTGAAATACTCGGGCTTAACCTGGGTGCTGCATTCCAAACTGGATATCTAGAGTGCAGGAGAGGAAAGTAGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAATACCAGTGGCGAAGGCGACTTTCTGGACTGTAACTGACACTGAGGCTCGAAAGCGTGGGG
## 51: GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGCGTGCAGCCGGGTCTGCAAGTCAGATGTGAAATCCATGGGCTCAACCCATGAACTGCATTTGAAACTGTAGATCTTGAGTGTCGGAGGGGCAATCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGATTGCTGGACGATAACTGACGGTGAGGCGCGAAAGTGTGGGG
## 52: GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGCGTGTAGCCGGGAGGGCAAGTCAGATGTGAAATCCACGGGCTCAACTCGTGAACTGCATTTGAAACTACTCTTCTTGAGTATCGGAGAGGCAATCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGATTGCTGGACGACAACTGACGGTGAGGCGCGAAAGCGTGGGG
## 53: GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGATTGGCAAGTCAGAAGTGAAATCCATGGGCTTAACCCATGAACTGCTTTTGAAACTGTTAGTCTTGAGTGAAGTAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGAAATGCGTAGAGATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCTTTAACTGACGCTGAGGCACGAAAGTGTGGGT
## 54: GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT
## 55: GCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGAAGAATAAGTCTGATGTGAAAGCCCTCGGCTTAACCGAGGAACTGCATCGGAAACTGTTTTTCTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT
## 56: GCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGAATGATAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAACTGCATCGGAAACTGTCATTCTTGAGTGCAGAAGAGGAGAGTGGAATTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT
## 57: GCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGAGAAATAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAACTGCATCGGAAACTGTTTTTCTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT
## 58: GCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGG
## 59: GCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATCGGAAACTGGGAAACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCATGGGT
## 60: GCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTCTTAGGTCTGATGTGAAAGCCTTCGGCTTAACCGGAGAAGTGCATCGGAAACCAGGAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCATGGGT
## 61: GCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTTTTAAGTCTGATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATCGGAAACTGGGAAACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGTATGGGT
## 62: GCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGTGCAGGCGGTTCAATAAGTCTGATGTGAAAGCCTTCGGCTCAACCGGAGAATTGCATCAGAAACTGTTGAACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGT
## 63: GCAAGCGTTGTCCGGATTTATTGGGCGTAAAGGGCTCGTAGGCGGTTTGTTGCGTCTGGTGTGAAAGCTTACTGCTTAACGGTAGGTTGCGCTGGATACGGGCAGGCTTGAGTGCAGTAGGGGAGACTGGAATTCTCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACACCTATGGCGAAGGCAGGTCTCTGGGCTGTTACTGACGCTGAGGAGCGAAAGCGTGGGG
## 64: GCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTGGGTAAGACAGATGTGAAATCCCCGGGCTTAACCTGGGAACTGCATTTGTGACTGTCCGACTGGAGTATGTCAGAGGGGGGTGGAATTCCAAGTGTAGCAGTGAAATGCGTAGATATTTGGAAGAACACCGATGGCGAAGGCAGCCCCCTGGGGCAAAACTGACGCTCATGCACGAAAGCGTGGGG
## 65: GCGAGCGTTAATCGGAATTACTGGGCGTAAAGGGTGCGCAGGCGGTTGAGTAAGACAGATGTGAAATCCCCGAGCTTAACTCGGGAATGGCATATGTGACTGCTCGACTAGAGTGTGTCAGAGGGAGGTGGAATTCCACGTGTAGCAGTGAAATGCGTAGATATGTGGAAGAACACCGATGGCGAAGGCAGCCTCCTGGGACATAACTGACGCTCAGGCACGAAAGCGTGGGG
## 66: GCGAGCGTTATCCGGAATGATTGGGCGTAAAGGGTGCGTAGGTGGCAGATCAAGTCTGGAGTAAAAGGTATGGGCTCAACCCGTACTGGCTCTGGAAACTGATCAGCTAGAGAACAGAAGAGGACGGCGGAACTCCATGTGTAGCGGTAAAATGCGTAGATATATGGAAGAACACCGGTGGCGAAGGCGGCCGTCTGGTCTGGATTCTGACACTGAAGCACGAAAGCGTGGGG
## 67: GCGAGCGTTATCCGGAATTATTGGGCGTAAAGAGGGAGCAGGCGGCACTAAGGGTCTGTGGTGAAAGATCGAAGCTTAACTTCGGTAAGCCATGGAAACCGTAGAGCTAGAGTGTGTGAGAGGATCGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAGGCGACGATCTGGCGCATAACTGACGCTCAGTCCCGAAAGCGTGGGG
## 68: GCGAGCGTTATCCGGATTTACTGGGCGTAAAGGATGCGTAGGTGGAATTTTAAGTGGGATGTGAAATACCCGGGCTCAACCTGGGAACTGCATTCCAAACTGGAATTCTAGAGTGCAGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACACTGAGGCATGAAAGCGTGGGG
## 69: GCGAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGTAGGCGGGAATGCAAGTCAGATGTGAAATCCAGGGGCTTAACCCTTGAACTGCATTTGAAACTGTATTTCTTGAGTGTCGGAGAGGTTGACGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGTCAACTGGACGATAACTGACGCTGAGGCGCGAAAGCGTGGGG
## 70: GCGAGCGTTATCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGTTTGTTAAGTCAGAAGTGAAATTTAGGGGCTCAACCTCTAAGCTGCTTCTGAAACTGATGAACTAGAGTGTGGGAGAGGAAAGTGGAATTCCGAGTGTAGCGGTGAAATGCGTAGAGATTCGGAGGAACACCAGTAGCGAAGGCGGCTTTCTGGACCATAACTGACGCTGAGGCACGAAAGCGTGGGG
## 71: GCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGCAGACGGGAGATTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGTTTCCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACCCCGATTGCGAAGGCAGCTTGCTAAACTGTAACTGACGTTCATGCTCGAAAGTGTGGGT
## 72: GCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGCAGACGGGGGATTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGTTCCCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCATAGATATCACGAAGAACCCCGATTGCGAAGGCAGCCTGCTAAGCTGTAACTGACGTTGAGGCTCGAAAGTGTGGGT
## 73: GCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCAAGGTAAGTCAGCGGTGAAAGACCAGGGCTCAACTCTGGAAGTGCCGTTGATACTGTCTGGCTAGAATGATTCCGCCGTGGGAGGAATGAGTAGTGTAGCGGTGAAATGCATAGATATTACTCAGAACACCGATTGCGAAGGCATCTCACGAGGGGTTCATTGACGCTGAGGCACGAAAGCGTGGGG
## 74: GCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCACGCCAAGTCAGCGGTGAAATTTTCGGGCTCAACCCGGACTGTGCCGTTGAAACTGGCGAGCTAGAGTGCACAAGAGGCAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCCTGCTAGGGTGCGACAGACGCTGAGGCACGAAAGCGTGGGT
## 75: GCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTGGTGATTTAAGTCAGCGGTGAAAGTTTGTGGCTCAACCATAAAATTGCCGTTGAAACTGGGTTACTTGAGTGTGTTTGAGGTAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCTTACTAAACCATAACTGACACTGAAGCACGAAAGCGTGGGG
## 76: GCGAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGTAGGCGGGACGGCAAGTCAGATGTGAAAACTATGGGCTCAACCCATAGACTGCATTTGAAACTGTTGTTCTTGAGTGAGGTAGAGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGAGATCAGGAGGAACATCGGTGGCGAAGGCGGCTTACTGGGCCTTTACTGACGCTGAGGCTCGAAAGCGTGGGT
## 77: GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCTTGTAGGCGGTTTGTCGCGTCTGCTGTGAAAGGCCGGAGCTTAACTCCGTGTATTGCAGTGGGTACGGGCAGACTAGAGTGCAGTAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGGTCTCTGGGCTGTAACTGACGCTGAGAAGCGAAAGCATGGGG
## 78: GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCTTGTAGGCGGTTTGTCGCGTCTGCTGTGAAAGGCCGGGGCTTAACCCCGTGTATTGCAGTGGGTACGGGCAGACTAGAGTGCAGTAGGGGAGACTGGAACTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAAGAACACCGATGGCGAAGGCAGGTCTCTGGGCTGTAACTGACGCTGAGAAGCGAAAGCATGGGG
## 79: GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCTTGTAGGCGGTTTGTCGCGTCTGCTGTGAAAGGCCGGGGCTTAACTCCGTGTATTGCAGTGGGTACGGGCAGACTAGAGTGCAGTAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGGTCTCTGGGCTGTAACTGACGCTGAGAAGCGAAAGCATGGGG
## 80: GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAGGTAAGTCTATCTTAAAAGTGCGGGGCTCAACCCCGTGAGGGGATGGAAACTATCTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGG
## 81: GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTTGTAGGCGGTTGGTCGCGTCTGCCGTGAAATCCTCTGGCTTAACTGGGGGCGTGCGGTGGGTACGGGCTGACTTGAGTGCGGTAGGGGAGACTGGAACTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAAGAACACCGGTGGCGAAGGCGGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGG
## 82: GCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTTGTAGGCGGTTTGTCGCGTCTGCCGTGAAATCCTCTGGCTTAACTGGGGGCGTGCGGTGGGTACGGGCAGGCTTGAGTGCGGTAGGGGAGACTGGAACTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAAGAACACCGGTGGCGAAGGCGGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGG
## 83: GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGAAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT
## 84: GCGAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGACCAGTAAGTCTGTCGTCAAAGGCGGAGGCTCAACCTTCGTTCCACGATAGATACTGCGGGTCTAGAGTATGTGAGAGGGAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGCACACAACTGACGCTCATGTGCGAAAGCCAGGGC
## 85: GCGGTAACACAAAGAGGGCGAGCGTTAATCATAATGGTTTAAAGGATCCGTAGAATGAATTATATATTATAATTTAGAGTTAATAAAATTAATTAAAGAATTATAATAGTAAAGATGAAATAATAATAATAATTATAAGACTAATATATGTGAAAATATTAATTAAATATTAACTGACATTGAGGGATTAAAACTAGAGTAGCGAAACGGATTAGAAACCCGTGTAGTCCGGCTGAC
## 86: GCTAGCGTTATCCGGAATTACTGGGCGTAAAGGGTGCGTAGGTGGTTTCTTAAGTCAGAGGTGAAAGGCTACGGCTCAACCGTAGTAAGCCTTTGAAACTGGGAAACTTGAGTGCAGGAGAGGAGAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTTGCGAAGGCGGCTCTCTGGACTGTAACTGACACTGAGGCACGAAAGCGTGGGG
## 87: GCTAGCGTTATCCGGATTTACTGGGCGTAAAGGGTGCGTAGGCGGTCTTTTAAGTCAGGAGTGAAAGGCTACGGCTCAACCGTAGTAAGCTCTTGAAACTGGAGGACTTGAGTGCAGGAGAGGAGAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTAGCGAAGGCGGCTCTCTGGACTGTAACTGACGCTGAGGCACGAAAGCGTGGGG
## 88: TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG
## OTU
## Kingdom Phylum Class
## 1: Bacteria Firmicutes Clostridia
## 2: Bacteria Firmicutes Clostridia
## 3: Bacteria Bacteroidetes Bacteroidia
## 4: Bacteria Firmicutes Bacilli
## 5: Bacteria Firmicutes Bacilli
## 6: Bacteria Firmicutes Bacilli
## 7: Bacteria Bacteroidetes Bacteroidia
## 8: Bacteria Bacteroidetes Bacteroidia
## 9: Bacteria Bacteroidetes Bacteroidia
## 10: Bacteria Bacteroidetes Bacteroidia
## 11: Bacteria Firmicutes Bacilli
## 12: Bacteria Firmicutes Bacilli
## 13: Bacteria Bacteroidetes Bacteroidia
## 14: Bacteria Bacteroidetes Bacteroidia
## 15: Bacteria Bacteroidetes Bacteroidia
## 16: Bacteria Bacteroidetes Bacteroidia
## 17: Bacteria Bacteroidetes Bacteroidia
## 18: Bacteria Proteobacteria Deltaproteobacteria
## 19: Bacteria Proteobacteria Gammaproteobacteria
## 20: Bacteria Proteobacteria Gammaproteobacteria
## 21: Bacteria Proteobacteria Betaproteobacteria
## 22: Bacteria Proteobacteria Betaproteobacteria
## 23: Bacteria Firmicutes Erysipelotrichia
## 24: Bacteria Firmicutes Bacilli
## 25: Bacteria Actinobacteria Actinobacteria
## 26: Bacteria Actinobacteria Actinobacteria
## 27: Bacteria Firmicutes Clostridia
## 28: Bacteria Firmicutes Clostridia
## 29: Bacteria Firmicutes Clostridia
## 30: Bacteria Firmicutes Clostridia
## 31: Bacteria Firmicutes Clostridia
## 32: Bacteria Firmicutes Clostridia
## 33: Bacteria Firmicutes Clostridia
## 34: Bacteria Firmicutes Clostridia
## 35: Bacteria Firmicutes Clostridia
## 36: Bacteria Firmicutes Clostridia
## 37: Bacteria Firmicutes Clostridia
## 38: Bacteria Firmicutes Clostridia
## 39: Bacteria Firmicutes Clostridia
## 40: Bacteria Firmicutes Bacilli
## 41: Bacteria Firmicutes Bacilli
## 42: Bacteria Firmicutes Clostridia
## 43: Bacteria Firmicutes Negativicutes
## 44: Bacteria Firmicutes Negativicutes
## 45: Bacteria Firmicutes Negativicutes
## 46: Bacteria Firmicutes Bacilli
## 47: Bacteria Firmicutes Negativicutes
## 48: Bacteria Firmicutes Negativicutes
## 49: Bacteria Firmicutes Clostridia
## 50: Bacteria Firmicutes Clostridia
## 51: Bacteria Firmicutes Clostridia
## 52: Bacteria Firmicutes Clostridia
## 53: Bacteria Firmicutes Clostridia
## 54: Bacteria Firmicutes Clostridia
## 55: Bacteria Firmicutes Bacilli
## 56: Bacteria Firmicutes Bacilli
## 57: Bacteria Firmicutes Bacilli
## 58: Bacteria Firmicutes Bacilli
## 59: Bacteria Firmicutes Bacilli
## 60: Bacteria Firmicutes Bacilli
## 61: Bacteria Firmicutes Bacilli
## 62: Bacteria Firmicutes Bacilli
## 63: Bacteria Actinobacteria Actinobacteria
## 64: Bacteria Proteobacteria Betaproteobacteria
## 65: Bacteria Proteobacteria Betaproteobacteria
## 66: Bacteria Firmicutes Erysipelotrichia
## 67: Bacteria Firmicutes Erysipelotrichia
## 68: Bacteria Firmicutes Clostridia
## 69: Bacteria Firmicutes Clostridia
## 70: Bacteria Firmicutes Clostridia
## 71: Bacteria Bacteroidetes Bacteroidia
## 72: Bacteria Bacteroidetes Bacteroidia
## 73: Bacteria Bacteroidetes Bacteroidia
## 74: Bacteria Bacteroidetes Bacteroidia
## 75: Bacteria Bacteroidetes Bacteroidia
## 76: Bacteria Firmicutes Clostridia
## 77: Bacteria Actinobacteria Actinobacteria
## 78: Bacteria Actinobacteria Actinobacteria
## 79: Bacteria Actinobacteria Actinobacteria
## 80: Bacteria Firmicutes Negativicutes
## 81: Bacteria Actinobacteria Actinobacteria
## 82: Bacteria Actinobacteria Actinobacteria
## 83: Bacteria Firmicutes Bacilli
## 84: Bacteria Synergistetes Synergistia
## 85: Bacteria Proteobacteria Gammaproteobacteria
## 86: Bacteria Firmicutes Clostridia
## 87: Bacteria Firmicutes Clostridia
## 88: Bacteria Verrucomicrobia Verrucomicrobiae
## Kingdom Phylum Class
## Order Family
## 1: Clostridiales Ruminococcaceae
## 2: Clostridiales Ruminococcaceae
## 3: Bacteroidales Prevotellaceae
## 4: Lactobacillales Leuconostocaceae
## 5: Lactobacillales Leuconostocaceae
## 6: Lactobacillales Streptococcaceae
## 7: Bacteroidales Bacteroidaceae
## 8: Bacteroidales Bacteroidaceae
## 9: Bacteroidales Bacteroidaceae
## 10: Bacteroidales Bacteroidaceae
## 11: Lactobacillales Streptococcaceae
## 12: Lactobacillales Streptococcaceae
## 13: Bacteroidales Prevotellaceae
## 14: Bacteroidales Prevotellaceae
## 15: Bacteroidales Prevotellaceae
## 16: Bacteroidales Prevotellaceae
## 17: Bacteroidales Prevotellaceae
## 18: Desulfovibrionales Desulfovibrionaceae
## 19: Enterobacteriales Enterobacteriaceae
## 20: Enterobacteriales Enterobacteriaceae
## 21: Burkholderiales Burkholderiaceae
## 22: Burkholderiales Sutterellaceae
## 23: Erysipelotrichales Erysipelotrichaceae
## 24: Bacillales Bacillaceae_1
## 25: Bifidobacteriales Bifidobacteriaceae
## 26: Bifidobacteriales Bifidobacteriaceae
## 27: Clostridiales Ruminococcaceae
## 28: Clostridiales Lachnospiraceae
## 29: Clostridiales Lachnospiraceae
## 30: Clostridiales Lachnospiraceae
## 31: Clostridiales Lachnospiraceae
## 32: Clostridiales Lachnospiraceae
## 33: Clostridiales Lachnospiraceae
## 34: Clostridiales Lachnospiraceae
## 35: Clostridiales Lachnospiraceae
## 36: Clostridiales Ruminococcaceae
## 37: Clostridiales Ruminococcaceae
## 38: Clostridiales Lachnospiraceae
## 39: Clostridiales Lachnospiraceae
## 40: Lactobacillales Lactobacillaceae
## 41: Lactobacillales Lactobacillaceae
## 42: Clostridiales Ruminococcaceae
## 43: Selenomonadales Acidaminococcaceae
## 44: Selenomonadales Veillonellaceae
## 45: Selenomonadales Veillonellaceae
## 46: Bacillales Bacillales_Incertae_Sedis_XI
## 47: Selenomonadales Veillonellaceae
## 48: Selenomonadales Veillonellaceae
## 49: Clostridiales Clostridiaceae_1
## 50: Clostridiales Clostridiaceae_1
## 51: Clostridiales Ruminococcaceae
## 52: Clostridiales Ruminococcaceae
## 53: Clostridiales Ruminococcaceae
## 54: Clostridiales Ruminococcaceae
## 55: Lactobacillales Lactobacillaceae
## 56: Lactobacillales Lactobacillaceae
## 57: Lactobacillales Lactobacillaceae
## 58: Lactobacillales Enterococcaceae
## 59: Lactobacillales Lactobacillaceae
## 60: Lactobacillales Lactobacillaceae
## 61: Lactobacillales Lactobacillaceae
## 62: Lactobacillales Lactobacillaceae
## 63: Bifidobacteriales Bifidobacteriaceae
## 64: Burkholderiales Sutterellaceae
## 65: Burkholderiales Sutterellaceae
## 66: Erysipelotrichales Erysipelotrichaceae
## 67: Erysipelotrichales Erysipelotrichaceae
## 68: Clostridiales Clostridiaceae_1
## 69: Clostridiales Ruminococcaceae
## 70: Clostridiales Lachnospiraceae
## 71: Bacteroidales Bacteroidaceae
## 72: Bacteroidales Bacteroidaceae
## 73: Bacteroidales Marinilabiliaceae
## 74: Bacteroidales Porphyromonadaceae
## 75: Bacteroidales Porphyromonadaceae
## 76: Clostridiales Ruminococcaceae
## 77: Actinomycetales Micrococcaceae
## 78: Actinomycetales Micrococcaceae
## 79: Actinomycetales Micrococcaceae
## 80: Selenomonadales Veillonellaceae
## 81: Actinomycetales Actinomycetaceae
## 82: Actinomycetales Actinomycetaceae
## 83: Lactobacillales Lactobacillaceae
## 84: Synergistales Synergistaceae
## 85: Gammaproteobacteria_incertae_sedis Candidatus_Carsonella
## 86: Clostridiales Peptostreptococcaceae
## 87: Clostridiales Peptostreptococcaceae
## 88: Verrucomicrobiales Verrucomicrobiaceae
## Order Family
## Genus Species baseMean log2FoldChange
## 1: Faecalibacterium prausnitzii 3.0343248 -4.08667447
## 2: Faecalibacterium prausnitzii 12.4200116 0.07383313
## 3: Prevotella NA 1.4218562 -2.99038716
## 4: Fructobacillus fructosus 0.6069870 -1.45628345
## 5: Leuconostoc NA 0.7910991 -2.16757269
## 6: Streptococcus NA 7.2220258 0.15650568
## 7: Bacteroides NA 6.1742670 -5.10177978
## 8: Bacteroides massiliensis 1.4127406 -2.95432416
## 9: Bacteroides NA 2.1181649 -3.56730011
## 10: Bacteroides ovatus 2.0500179 5.87546311
## 11: Streptococcus NA 141.8212152 -1.07783869
## 12: Lactococcus NA 4.9813725 4.71444079
## 13: Prevotella copri 23.6546362 -7.04218661
## 14: Prevotella NA 0.1355131 -0.38378361
## 15: Prevotella NA 1.2196181 -2.79338036
## 16: Prevotella NA 1.5177211 -3.06839238
## 17: Prevotella NA 0.5526678 -1.45628345
## 18: Bilophila wadsworthia 0.4065394 -1.32959095
## 19: NA NA 4.7146402 -0.54875931
## 20: Escherichia/Shigella NA 884.6984782 9.15519367
## 21: Burkholderia NA 1.5174676 -3.04247689
## 22: Sutterella NA 0.9485919 -2.43806135
## 23: Clostridium_XVIII ramosum 0.2928597 3.08858530
## 24: Bacillus NA 0.6328793 -1.85130097
## 25: Bifidobacterium NA 0.9137253 4.69741388
## 26: Bifidobacterium NA 29.5647938 -4.19589952
## 27: Clostridium_IV NA 0.6908348 -1.88614607
## 28: Roseburia NA 6.3585490 -0.08032018
## 29: Fusicatenibacter NA 0.7614378 4.43272462
## 30: Clostridium_XlVa NA 1.0507300 -2.53265427
## 31: Dorea formicigenerans 1.0426945 -2.54411530
## 32: Clostridium_XlVa NA 0.4065394 -1.32959095
## 33: NA NA 0.3045751 3.09643502
## 34: NA NA 0.3164397 -1.06246727
## 35: NA NA 0.2373297 -0.81386196
## 36: Flavonifractor plautii 1.5005720 -3.05642061
## 37: Pseudoflavonifractor NA 0.2108480 -0.38378361
## 38: Coprococcus NA 1.1064372 -2.61659006
## 39: Coprococcus NA 1.2435027 -2.75933626
## 40: Lactobacillus NA 0.9137253 4.69741388
## 41: Pediococcus NA 245.1927825 -23.83234880
## 42: NA NA 0.3164397 -1.06246727
## 43: Acidaminococcus NA 1.2135287 3.63773402
## 44: Veillonella NA 1.1866487 -2.74436048
## 45: Dialister NA 2.5541222 0.30398504
## 46: Gemella NA 4.3281375 -4.59513716
## 47: Megamonas funiformis 0.9671687 -2.38760457
## 48: Megasphaera NA 0.8702090 -2.30291512
## 49: Clostridium_sensu_stricto cellulovorans 0.7910991 -2.16757269
## 50: Clostridium_sensu_stricto NA 0.2052102 -0.75316800
## 51: NA NA 1.8477075 1.97926525
## 52: Oscillibacter NA 0.4746595 -1.48540031
## 53: Clostridium_IV NA 0.4669911 -1.40253114
## 54: Ruminococcus NA 0.9431474 1.68420434
## 55: Lactobacillus NA 4.8692199 3.68469522
## 56: Lactobacillus delbrueckii 8.7316588 4.35686608
## 57: Lactobacillus kalixensis 0.9339822 -2.36063263
## 58: Enterococcus NA 0.4065394 -1.32959095
## 59: Lactobacillus NA 11.8513219 -6.04952081
## 60: Lactobacillus NA 0.6328793 -1.85130097
## 61: Lactobacillus NA 183.9223070 -1.69484438
## 62: Lactobacillus NA 1.7571582 5.65369332
## 63: Scardovia wiggsiae 0.4930847 2.81586971
## 64: NA NA 0.8130787 -2.22088019
## 65: Parasutterella excrementihominis 0.4145009 -0.81386196
## 66: Holdemanella NA 0.2843712 -0.81386196
## 67: Clostridium_XVIII NA 0.5837389 -1.67941216
## 68: Clostridium_sensu_stricto cadaveris 0.7119892 -2.01813080
## 69: NA NA 0.7004867 -1.93938057
## 70: Cellulosilyticum lentocellum 0.3164397 -1.06246727
## 71: Bacteroides coprocola 0.4746595 -1.48540031
## 72: Bacteroides NA 1.3816696 -2.91458861
## 73: Anaerophaga NA 0.1582198 -0.38378361
## 74: Barnesiella NA 0.4145009 -0.81386196
## 75: Parabacteroides merdae 1.2676146 -2.81318756
## 76: Ruminococcus NA 0.6091502 4.10833964
## 77: Rothia mucilaginosa 0.9104805 -2.28159316
## 78: Rothia mucilaginosa 0.2565127 -0.92894597
## 79: Rothia mucilaginosa 2.8571428 -3.99686873
## 80: Mitsuokella jalaludinii 0.1582198 -0.38378361
## 81: Actinomyces odontolyticus 19.7583316 -6.78109238
## 82: Actinomyces NA 3.7733590 2.13611203
## 83: Lactobacillus ruminis 0.6325439 -1.80811983
## 84: Cloacibacillus evryensis 0.2763339 -0.38378361
## 85: NA NA 0.1582198 -0.38378361
## 86: Romboutsia NA 1.1702608 -2.71992544
## 87: Intestinibacter bartlettii 0.7119892 -2.01813080
## 88: Akkermansia muciniphila 1.6189994 -3.15371731
## Genus Species baseMean log2FoldChange
## lfcSE stat pvalue padj Significant
## 1: 3.893324 -1.04966196 2.938736e-01 9.520388e-01 FALSE
## 2: 3.345390 0.02207011 9.823920e-01 9.823920e-01 FALSE
## 3: 3.903272 -0.76612311 4.436031e-01 9.520388e-01 FALSE
## 4: 3.935468 -0.37004075 7.113521e-01 9.520388e-01 FALSE
## 5: 3.917506 -0.55330418 5.800551e-01 9.520388e-01 FALSE
## 6: 3.634720 0.04305852 9.656549e-01 9.823920e-01 FALSE
## 7: 3.324124 -1.53477404 1.248393e-01 9.520388e-01 FALSE
## 8: 3.903743 -0.75679260 4.491741e-01 9.520388e-01 FALSE
## 9: 3.897122 -0.91536789 3.599985e-01 9.520388e-01 FALSE
## 10: 3.695263 1.58999850 1.118351e-01 9.520388e-01 FALSE
## 11: 2.144040 -0.50271379 6.151655e-01 9.520388e-01 FALSE
## 12: 3.658512 1.28862237 1.975294e-01 9.520388e-01 FALSE
## 13: 3.885654 -1.81235542 6.993130e-02 9.520388e-01 FALSE
## 14: 3.949885 -0.09716325 9.225968e-01 9.665299e-01 FALSE
## 15: 3.905993 -0.71515239 4.745149e-01 9.520388e-01 FALSE
## 16: 3.902292 -0.78630513 4.316887e-01 9.520388e-01 FALSE
## 17: 3.935468 -0.37004075 7.113521e-01 9.520388e-01 FALSE
## 18: 3.938388 -0.33759772 7.356664e-01 9.520388e-01 FALSE
## 19: 3.665669 -0.14970238 8.809994e-01 9.665299e-01 FALSE
## 20: 3.358512 2.72596689 6.411343e-03 2.820991e-01 FALSE
## 21: 3.902612 -0.77960013 4.356263e-01 9.520388e-01 FALSE
## 22: 3.911926 -0.62323807 5.331281e-01 9.520388e-01 FALSE
## 23: 3.794537 0.81395569 4.156703e-01 9.520388e-01 FALSE
## 24: 3.925467 -0.47161289 6.372031e-01 9.520388e-01 FALSE
## 25: 3.716779 1.26383987 2.062875e-01 9.520388e-01 FALSE
## 26: 2.927460 -1.43328998 1.517750e-01 9.520388e-01 FALSE
## 27: 3.924505 -0.48060742 6.307955e-01 9.520388e-01 FALSE
## 28: 3.583433 -0.02241431 9.821175e-01 9.823920e-01 FALSE
## 29: 3.724506 1.19015108 2.339870e-01 9.520388e-01 FALSE
## 30: 3.910204 -0.64770384 5.171765e-01 9.520388e-01 FALSE
## 31: 3.910003 -0.65066838 5.152606e-01 9.520388e-01 FALSE
## 32: 3.938388 -0.33759772 7.356664e-01 9.520388e-01 FALSE
## 33: 3.793917 0.81615773 4.144099e-01 9.520388e-01 FALSE
## 34: 3.943331 -0.26943394 7.875958e-01 9.665299e-01 FALSE
## 35: 3.946722 -0.20621211 8.366252e-01 9.665299e-01 FALSE
## 36: 3.902439 -0.78320773 4.335051e-01 9.520388e-01 FALSE
## 37: 3.949885 -0.09716325 9.225968e-01 9.665299e-01 FALSE
## 38: 3.908766 -0.66941586 5.032302e-01 9.520388e-01 FALSE
## 39: 3.906502 -0.70634460 4.799739e-01 9.520388e-01 FALSE
## 40: 3.716779 1.26383987 2.062875e-01 9.520388e-01 FALSE
## 41: 3.884625 -6.13504511 8.513503e-10 7.491883e-08 TRUE
## 42: 3.943331 -0.26943394 7.875958e-01 9.665299e-01 FALSE
## 43: 3.709451 0.98066654 3.267572e-01 9.520388e-01 FALSE
## 44: 3.906729 -0.70247016 4.823860e-01 9.520388e-01 FALSE
## 45: 3.680308 0.08259772 9.341714e-01 9.671422e-01 FALSE
## 46: 3.296026 -1.39414455 1.632740e-01 9.520388e-01 FALSE
## 47: 3.912891 -0.61018938 5.417364e-01 9.520388e-01 FALSE
## 48: 3.914587 -0.58829077 5.563371e-01 9.520388e-01 FALSE
## 49: 3.917506 -0.55330418 5.800551e-01 9.520388e-01 FALSE
## 50: 3.947287 -0.19080652 8.486772e-01 9.665299e-01 FALSE
## 51: 3.676892 0.53829837 5.903711e-01 9.520388e-01 FALSE
## 52: 3.934769 -0.37750633 7.057974e-01 9.520388e-01 FALSE
## 53: 3.936792 -0.35626245 7.216440e-01 9.520388e-01 FALSE
## 54: 3.749966 0.44912519 6.533414e-01 9.520388e-01 FALSE
## 55: 3.641183 1.01194993 3.115620e-01 9.520388e-01 FALSE
## 56: 3.631788 1.19964782 2.302761e-01 9.520388e-01 FALSE
## 57: 3.913420 -0.60321466 5.463659e-01 9.520388e-01 FALSE
## 58: 3.938388 -0.33759772 7.356664e-01 9.520388e-01 FALSE
## 59: 3.886781 -1.55643469 1.196048e-01 9.520388e-01 FALSE
## 60: 3.925467 -0.47161289 6.372031e-01 9.520388e-01 FALSE
## 61: 3.609592 -0.46953905 6.386844e-01 9.520388e-01 FALSE
## 62: 3.698104 1.52880883 1.263118e-01 9.520388e-01 FALSE
## 63: 3.765422 0.74782320 4.545668e-01 9.520388e-01 FALSE
## 64: 3.916324 -0.56708280 5.706579e-01 9.520388e-01 FALSE
## 65: 3.946722 -0.20621211 8.366252e-01 9.665299e-01 FALSE
## 66: 3.946722 -0.20621211 8.366252e-01 9.665299e-01 FALSE
## 67: 3.930146 -0.42731542 6.691496e-01 9.520388e-01 FALSE
## 68: 3.921057 -0.51469052 6.067693e-01 9.520388e-01 FALSE
## 69: 3.923077 -0.49435190 6.210577e-01 9.520388e-01 FALSE
## 70: 3.943331 -0.26943394 7.875958e-01 9.665299e-01 FALSE
## 71: 3.934769 -0.37750633 7.057974e-01 9.520388e-01 FALSE
## 72: 3.904276 -0.74651190 4.553582e-01 9.520388e-01 FALSE
## 73: 3.949885 -0.09716325 9.225968e-01 9.665299e-01 FALSE
## 74: 3.946722 -0.20621211 8.366252e-01 9.665299e-01 FALSE
## 75: 3.905703 -0.72027691 4.713545e-01 9.520388e-01 FALSE
## 76: 3.736091 1.09963595 2.714908e-01 9.520388e-01 FALSE
## 77: 3.915029 -0.58277810 5.600427e-01 9.520388e-01 FALSE
## 78: 3.945106 -0.23546792 8.138456e-01 9.665299e-01 FALSE
## 79: 3.893888 -1.02644678 3.046810e-01 9.520388e-01 FALSE
## 80: 3.949885 -0.09716325 9.225968e-01 9.665299e-01 FALSE
## 81: 3.164536 -2.14283959 3.212598e-02 9.423621e-01 FALSE
## 82: 3.641154 0.58665799 5.574334e-01 9.520388e-01 FALSE
## 83: 3.926692 -0.46046897 6.451796e-01 9.520388e-01 FALSE
## 84: 3.949885 -0.09716325 9.225968e-01 9.665299e-01 FALSE
## 85: 3.949885 -0.09716325 9.225968e-01 9.665299e-01 FALSE
## 86: 3.907105 -0.69614855 4.863358e-01 9.520388e-01 FALSE
## 87: 3.921057 -0.51469052 6.067693e-01 9.520388e-01 FALSE
## 88: 3.901278 -0.80838051 4.188716e-01 9.520388e-01 FALSE
## lfcSE stat pvalue padj Significantresdt.dds.d0.broad## OTU
## 1: ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 2: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
## 3: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
## 4: ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 5: ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
## ---
## 1586: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
## Kingdom Phylum Class Order
## 1: Bacteria Firmicutes Clostridia Clostridiales
## 2: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 3: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 4: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 5: Bacteria Firmicutes Clostridia Clostridiales
## ---
## 1586: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1587: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1588: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1589: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1590: Archaea Euryarchaeota Methanobacteria Methanobacteriales
## Family Genus Species baseMean
## 1: Ruminococcaceae NA NA 0
## 2: Fusobacteriaceae Fusobacterium nucleatum 0
## 3: Fusobacteriaceae Fusobacterium NA 0
## 4: Rikenellaceae NA NA 0
## 5: Eubacteriaceae Eubacterium NA 0
## ---
## 1586: Bacteroidaceae Bacteroides stercoris 0
## 1587: Bacteroidaceae Bacteroides NA 0
## 1588: Prevotellaceae Prevotella NA 0
## 1589: Prevotellaceae Prevotella bivia 0
## 1590: Methanobacteriaceae Methanobrevibacter NA 0
## log2FoldChange lfcSE stat pvalue padj Significant
## 1: NA NA NA NA NA NA
## 2: NA NA NA NA NA NA
## 3: NA NA NA NA NA NA
## 4: NA NA NA NA NA NA
## 5: NA NA NA NA NA NA
## ---
## 1586: NA NA NA NA NA NA
## 1587: NA NA NA NA NA NA
## 1588: NA NA NA NA NA NA
## 1589: NA NA NA NA NA NA
## 1590: NA NA NA NA NA NAvolcano.d0.broad.shed = ggplot(
data = resdt.dds.d0.broad[!is.na(Significant)][(pvalue < 1)],
mapping = aes(x = log2FoldChange,
y = -log10(pvalue),
color = Phylum,
label = OTU, label1 = Genus)) +
theme_bw() +
geom_point() +
geom_point(data = resdt.dds.d0.broad[(Significant)], size = 7, alpha = 0.7) +
# geom_text(data = resdt[(Significant)], mapping = aes(label = paste("Genus:", Genus)), color = "black", size = 3) +
theme(axis.text.x = element_text(angle = -90, hjust = 0, vjust=0.5)) +
geom_hline(yintercept = -log10(alpha)) +
ggtitle("DESeq2 Negative Binomial Test Volcano Plot\nDay 0 Broad Spectrum Antibiotics ~ Shedding") +
theme(axis.title = element_text(size=12)) +
theme(axis.text = element_text(size=12)) +
theme(legend.text = element_text(size=12)) +
geom_vline(xintercept = 0, lty = 2)
volcano.d0.broad.shed
summary(res.dds.d0.broad)##
## out of 88 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up) : 0, 0%
## LFC < 0 (down) : 1, 1.1%
## outliers [1] : 0, 0%
## low counts [2] : 34, 39%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?resultsmcols(res.dds.d0.broad, use.names = TRUE)## DataFrame with 6 rows and 2 columns
## type
## <character>
## baseMean intermediate
## log2FoldChange results
## lfcSE results
## stat results
## pvalue results
## padj results
## description
## <character>
## baseMean mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): Shedding Shedding vs No.shedding
## lfcSE standard error: Shedding Shedding vs No.shedding
## stat Wald statistic: Shedding Shedding vs No.shedding
## pvalue Wald test p-value: Shedding Shedding vs No.shedding
## padj BH adjusted p-valuesggplotly(volcano.d0.broad.shed)Shedding: Day 7 Narrow Spectrum Antibiotics
# Differential Abundance Testing
ds.d7.narrow.shed <- phyloseq_to_deseq2(ps1.d7.narrow, ~Shedding)
geoMeans.ds.d7.narrow.shed <- apply(counts(ds.d7.narrow.shed), 1, gm_mean)
ds.d7.narrow.shed <- estimateSizeFactors(ds.d7.narrow.shed, geoMeans = geoMeans.ds.d7.narrow.shed)
dds.d7.narrow.shed <- DESeq(ds.d7.narrow.shed, test="Wald", fitType="local", betaPrior = FALSE)
alpha = 0.05
# Tabulate and write results
res.dds.d7.narrow.shed = results(dds.d7.narrow.shed, cooksCutoff = FALSE)
sigtab_dds.dds.d7.narrow.shed = res.dds.d7.narrow.shed[which(res.dds.d7.narrow.shed$padj < alpha), ]
sigtab_dds.dds.d7.narrow.shed = cbind(as(sigtab_dds.dds.d7.narrow.shed, "data.frame"), as(tax_table(ps1.d7.narrow)[rownames(sigtab_dds.dds.d7.narrow.shed), ], "matrix"))
summary(res.dds.d7.narrow.shed)##
## out of 527 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up) : 107, 20%
## LFC < 0 (down) : 17, 3.2%
## outliers [1] : 0, 0%
## low counts [2] : 394, 75%
## (mean count < 2)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?resultshead(sigtab_dds.dds.d7.narrow.shed)## baseMean
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 317.6602
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG 1985.5854
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 509.0555
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGT 1657.9349
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT 789.6057
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 660.6060
## log2FoldChange
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT -26.363295
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG -6.156231
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 27.726154
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGT 8.504610
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT 11.863821
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 27.880344
## lfcSE
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 3.193587
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG 2.186104
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 3.127693
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGT 3.063343
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT 3.116180
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 3.127684
## stat
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT -8.255074
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG -2.816075
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 8.864731
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGT 2.776251
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT 3.807168
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 8.914055
## pvalue
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 1.518081e-16
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG 4.861439e-03
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 7.668889e-19
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGT 5.498972e-03
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT 1.405671e-04
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 4.919941e-19
## padj
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 4.675690e-15
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG 1.453712e-02
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 1.181009e-16
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGT 1.628542e-02
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT 4.286601e-04
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT 1.181009e-16
## Kingdom
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteria
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG Bacteria
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Bacteria
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGT Bacteria
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT Bacteria
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT Bacteria
## Phylum
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroidetes
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG Firmicutes
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Firmicutes
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGT Bacteroidetes
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT Fusobacteria
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT Firmicutes
## Class
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroidia
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG Clostridia
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Negativicutes
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGT Bacteroidia
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT Fusobacteriia
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT Clostridia
## Order
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroidales
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG Clostridiales
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Selenomonadales
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGT Bacteroidales
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT Fusobacteriales
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT Clostridiales
## Family
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroidaceae
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG Lachnospiraceae
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Veillonellaceae
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGT Bacteroidaceae
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT Fusobacteriaceae
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT Ruminococcaceae
## Genus
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroides
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG Blautia
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Dialister
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGT Bacteroides
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT Fusobacterium
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT Ruminococcus
## Species
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT <NA>
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGG <NA>
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG <NA>
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTAGACTGTTACTGACACTGATGCTCGAAAGTGTGGGT ovatus
## ACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTATAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT <NA>
## GCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAGCCTGCATTTGAAACTGCAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGT <NA>write.table(sigtab_dds.dds.d7.narrow.shed, file="./results/deseq_d7_narrow_Shedding.txt", sep = "\t") # Change filename to save results to appropriate file
# Quick check of factor levels
mcols(res.dds.d7.narrow.shed, use.names = TRUE)## DataFrame with 6 rows and 2 columns
## type
## <character>
## baseMean intermediate
## log2FoldChange results
## lfcSE results
## stat results
## pvalue results
## padj results
## description
## <character>
## baseMean mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): Shedding Shedding vs No.shedding
## lfcSE standard error: Shedding Shedding vs No.shedding
## stat Wald statistic: Shedding Shedding vs No.shedding
## pvalue Wald test p-value: Shedding Shedding vs No.shedding
## padj BH adjusted p-values# Prepare to join results data.table and taxonomy table
resdt.dds.d7.narrow.shed = data.table(as(results(dds.d7.narrow.shed, cooksCutoff = FALSE), "data.frame"),
keep.rownames = TRUE)
setnames(resdt.dds.d7.narrow.shed, "rn", "OTU")
taxdt.dds.d7.com = data.table(data.frame(as(tax_table(ps1.d7.narrow), "matrix")), keep.rownames = TRUE)
setnames(taxdt.dds.d7.com, "rn", "OTU")
# Join results data.table and taxonomy table
setkeyv(taxdt.dds.d7.com, "OTU")
setkeyv(resdt.dds.d7.narrow.shed, "OTU")
resdt.dds.d7.narrow.shed <- taxdt.dds.d7.com[resdt.dds.d7.narrow.shed]
resdt.dds.d7.narrow.shed## OTU
## 1: ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 2: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
## 3: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
## 4: ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 5: ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
## ---
## 1586: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
## Kingdom Phylum Class Order
## 1: Bacteria Firmicutes Clostridia Clostridiales
## 2: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 3: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 4: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 5: Bacteria Firmicutes Clostridia Clostridiales
## ---
## 1586: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1587: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1588: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1589: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1590: Archaea Euryarchaeota Methanobacteria Methanobacteriales
## Family Genus Species baseMean
## 1: Ruminococcaceae NA NA 0.000000
## 2: Fusobacteriaceae Fusobacterium nucleatum 2.102246
## 3: Fusobacteriaceae Fusobacterium NA 0.000000
## 4: Rikenellaceae NA NA 0.000000
## 5: Eubacteriaceae Eubacterium NA 0.000000
## ---
## 1586: Bacteroidaceae Bacteroides stercoris 0.000000
## 1587: Bacteroidaceae Bacteroides NA 0.000000
## 1588: Prevotellaceae Prevotella NA 28.552648
## 1589: Prevotellaceae Prevotella bivia 0.000000
## 1590: Methanobacteriaceae Methanobrevibacter NA 3.401384
## log2FoldChange lfcSE stat pvalue padj
## 1: NA NA NA NA NA
## 2: 4.948181 3.136987 1.577367 1.147110e-01 NA
## 3: NA NA NA NA NA
## 4: NA NA NA NA NA
## 5: NA NA NA NA NA
## ---
## 1586: NA NA NA NA NA
## 1587: NA NA NA NA NA
## 1588: 23.699942 3.128347 7.575868 3.567343e-14 3.924077e-13
## 1589: NA NA NA NA NA
## 1590: 4.134277 3.128144 1.321639 1.862883e-01 2.912528e-01resdt.dds.d7.narrow.shed[, Significant := padj < alpha]
resdt.dds.d7.narrow.shed[!is.na(Significant)]## OTU
## 1: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 2: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 3: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGATAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 4: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAGAACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 5: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTATGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## ---
## 304: TCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTGATAAGTTAGAGGTGAAATCCCGGGGCTTAACTCCGGAACTGCCTCTAATACTGTTAGACTAGAGAGTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCTTAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTATATCTGACGTTGAGGCACGAAAGCGTGGGG
## 305: TCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTGATAAGTTAGAGGTGAAATTTCGGGGCTCAACCCTGAACGTGCCTCTAATACTGTTGAGCTAGAGAGTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCTTAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTATATCTGACGTTGAGGCACGAAAGCGTGGGG
## 306: TCAAGCGTTGTTCGGAATCACTGGGCGTAAAGCGTGCGTAGGCTGTTTCGTAAGTCGTGTGTGAAAGGCGCGGGCTCAACCCGCGGACGGCACATGATACTGCGAGACTAGAGTAATGGAGGGGGAACCGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACTCGTGGCGAAGGCGGGTTCCTGGACATTAACTGACGCTGAGGCACGAAGGCCAGGGG
## 307: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 308: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
## Kingdom Phylum Class Order
## 1: Bacteria Firmicutes Clostridia Clostridiales
## 2: Bacteria Firmicutes Clostridia Clostridiales
## 3: Bacteria Firmicutes Clostridia Clostridiales
## 4: Bacteria Firmicutes Clostridia Clostridiales
## 5: Bacteria Firmicutes Clostridia Clostridiales
## ---
## 304: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 305: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 306: Bacteria Verrucomicrobia Verrucomicrobiae Verrucomicrobiales
## 307: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 308: Archaea Euryarchaeota Methanobacteria Methanobacteriales
## Family Genus Species baseMean
## 1: Ruminococcaceae Faecalibacterium prausnitzii 1295.374899
## 2: Ruminococcaceae Faecalibacterium prausnitzii 393.074688
## 3: Ruminococcaceae Faecalibacterium NA 8.445825
## 4: Ruminococcaceae Faecalibacterium prausnitzii 134.830487
## 5: Ruminococcaceae Faecalibacterium NA 2.687308
## ---
## 304: Rikenellaceae Alistipes NA 12.618977
## 305: Rikenellaceae Alistipes putredinis 12.685397
## 306: Verrucomicrobiaceae Akkermansia muciniphila 3634.940803
## 307: Prevotellaceae Prevotella NA 28.552648
## 308: Methanobacteriaceae Methanobrevibacter NA 3.401384
## log2FoldChange lfcSE stat pvalue padj
## 1: -2.7176525 3.060630 -0.8879390 3.745736e-01 5.196786e-01
## 2: 0.3278235 2.629898 0.1246526 9.007986e-01 9.350122e-01
## 3: 21.9907163 3.129995 7.0258003 2.128428e-12 9.932662e-12
## 4: -1.2160960 3.061475 -0.3972256 6.912011e-01 8.239888e-01
## 5: 5.2969525 3.134988 1.6896244 9.109983e-02 1.670164e-01
## ---
## 304: 22.1855474 3.129221 7.0897979 1.343080e-12 7.011334e-12
## 305: -7.0092234 3.195528 -2.1934478 2.827513e-02 7.507535e-02
## 306: 0.7666401 2.852488 0.2687619 7.881129e-01 8.731404e-01
## 307: 23.6999418 3.128347 7.5758680 3.567343e-14 3.924077e-13
## 308: 4.1342775 3.128144 1.3216393 1.862883e-01 2.912528e-01
## Significant
## 1: FALSE
## 2: FALSE
## 3: TRUE
## 4: FALSE
## 5: FALSE
## ---
## 304: TRUE
## 305: FALSE
## 306: FALSE
## 307: TRUE
## 308: FALSEresdt.dds.d7.narrow.shed## OTU
## 1: ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 2: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
## 3: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
## 4: ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 5: ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
## ---
## 1586: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
## Kingdom Phylum Class Order
## 1: Bacteria Firmicutes Clostridia Clostridiales
## 2: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 3: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 4: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 5: Bacteria Firmicutes Clostridia Clostridiales
## ---
## 1586: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1587: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1588: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1589: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1590: Archaea Euryarchaeota Methanobacteria Methanobacteriales
## Family Genus Species baseMean
## 1: Ruminococcaceae NA NA 0.000000
## 2: Fusobacteriaceae Fusobacterium nucleatum 2.102246
## 3: Fusobacteriaceae Fusobacterium NA 0.000000
## 4: Rikenellaceae NA NA 0.000000
## 5: Eubacteriaceae Eubacterium NA 0.000000
## ---
## 1586: Bacteroidaceae Bacteroides stercoris 0.000000
## 1587: Bacteroidaceae Bacteroides NA 0.000000
## 1588: Prevotellaceae Prevotella NA 28.552648
## 1589: Prevotellaceae Prevotella bivia 0.000000
## 1590: Methanobacteriaceae Methanobrevibacter NA 3.401384
## log2FoldChange lfcSE stat pvalue padj
## 1: NA NA NA NA NA
## 2: 4.948181 3.136987 1.577367 1.147110e-01 NA
## 3: NA NA NA NA NA
## 4: NA NA NA NA NA
## 5: NA NA NA NA NA
## ---
## 1586: NA NA NA NA NA
## 1587: NA NA NA NA NA
## 1588: 23.699942 3.128347 7.575868 3.567343e-14 3.924077e-13
## 1589: NA NA NA NA NA
## 1590: 4.134277 3.128144 1.321639 1.862883e-01 2.912528e-01
## Significant
## 1: NA
## 2: NA
## 3: NA
## 4: NA
## 5: NA
## ---
## 1586: NA
## 1587: NA
## 1588: TRUE
## 1589: NA
## 1590: FALSEvolcano.d7.narrow.shed = ggplot(
data = resdt.dds.d7.narrow.shed[!is.na(Significant)][(pvalue < 1)],
mapping = aes(x = log2FoldChange,
y = -log10(pvalue),
color = Phylum,
label = OTU, label1 = Genus)) +
theme_bw() +
geom_point() +
geom_point(data = resdt.dds.d7.narrow.shed[(Significant)], size = 7, alpha = 0.7) +
# geom_text(data = resdt[(Significant)], mapping = aes(label = paste("Genus:", Genus)), color = "black", size = 3) +
theme(axis.text.x = element_text(angle = -90, hjust = 0, vjust=0.5)) +
geom_hline(yintercept = -log10(alpha)) +
ggtitle("DESeq2 Negative Binomial Test Volcano Plot\nDay 7 Narrow Spectrum Antibiotics ~ Shedding") +
theme(axis.title = element_text(size=12)) +
theme(axis.text = element_text(size=12)) +
theme(legend.text = element_text(size=12)) +
geom_vline(xintercept = 0, lty = 2)
volcano.d7.narrow.shed
summary(res.dds.d7.narrow.shed)##
## out of 527 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up) : 107, 20%
## LFC < 0 (down) : 17, 3.2%
## outliers [1] : 0, 0%
## low counts [2] : 394, 75%
## (mean count < 2)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?resultsmcols(res.dds.d7.narrow.shed, use.names = TRUE)## DataFrame with 6 rows and 2 columns
## type
## <character>
## baseMean intermediate
## log2FoldChange results
## lfcSE results
## stat results
## pvalue results
## padj results
## description
## <character>
## baseMean mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): Shedding Shedding vs No.shedding
## lfcSE standard error: Shedding Shedding vs No.shedding
## stat Wald statistic: Shedding Shedding vs No.shedding
## pvalue Wald test p-value: Shedding Shedding vs No.shedding
## padj BH adjusted p-valuesggplotly(volcano.d7.narrow.shed)Shedding: Day 7 Broad Spectrum Antibiotics
sample_data(ps1)$day## [1] -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9
## [24] -9 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7
## [47] 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 0 0 0
## [70] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## [93] 0 0 0 0 0 0 0 0ps1.d7.broad <- subset_samples(ps1.broad, day == "7")
sample_data(ps1.d7.broad)$day## [1] 7 7 7 7 7 7 7 7 7 7 7 7 7
## Levels: 7sample_data(ps1.d7.broad)$randomization_arm## [1] Broad spectrum antibiotics Broad spectrum antibiotics
## [3] Broad spectrum antibiotics Broad spectrum antibiotics
## [5] Broad spectrum antibiotics Broad spectrum antibiotics
## [7] Broad spectrum antibiotics Broad spectrum antibiotics
## [9] Broad spectrum antibiotics Broad spectrum antibiotics
## [11] Broad spectrum antibiotics Broad spectrum antibiotics
## [13] Broad spectrum antibiotics
## Levels: Broad spectrum antibiotics# Differential Abundance Testing
ds.d7.broad <- phyloseq_to_deseq2(ps1.d7.broad, ~Shedding)
geoMeans.ds.d7.broad <- apply(counts(ds.d7.broad), 1, gm_mean)
ds.d7.broad <- estimateSizeFactors(ds.d7.broad, geoMeans = geoMeans.ds.d7.broad)
dds.d7.broad <- DESeq(ds.d7.broad, test="Wald", fitType="local", betaPrior = FALSE)
alpha = 0.05
# Tabulate and write results
res.dds.d7.broad = results(dds.d7.broad, cooksCutoff = FALSE)
sigtab_dds.dds.d7.broad = res.dds.d7.broad[which(res.dds.d7.broad$padj < alpha), ]
sigtab_dds.dds.d7.broad = cbind(as(sigtab_dds.dds.d7.broad, "data.frame"), as(tax_table(ps1.d7.broad)[rownames(sigtab_dds.dds.d7.broad), ], "matrix"))
summary(res.dds.d7.broad)##
## out of 365 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up) : 77, 21%
## LFC < 0 (down) : 9, 2.5%
## outliers [1] : 0, 0%
## low counts [2] : 316, 87%
## (mean count < 3)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?resultshead(sigtab_dds.dds.d7.broad)## baseMean
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 668.91942
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 166.40574
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 70.07518
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 709.05959
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTCAGGCTAGAGTGTCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGG 1577.61624
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 135.36504
## log2FoldChange
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 27.867029
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 7.627297
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 6.621713
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 27.949214
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTCAGGCTAGAGTGTCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGG 7.707301
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 8.600738
## lfcSE
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 3.051920
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 2.994864
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 2.784317
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 3.051917
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTCAGGCTAGAGTGTCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGG 2.968799
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 3.015846
## stat
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 9.130984
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 2.546792
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 2.378218
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 9.157921
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTCAGGCTAGAGTGTCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGG 2.596101
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 2.851849
## pvalue
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 6.787945e-20
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 1.087182e-02
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 1.739652e-02
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 5.290672e-20
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTCAGGCTAGAGTGTCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGG 9.428832e-03
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 4.346570e-03
## padj
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 5.871573e-18
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT 2.748332e-02
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT 4.067023e-02
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT 5.871573e-18
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTCAGGCTAGAGTGTCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGG 2.434609e-02
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG 1.174932e-02
## Kingdom
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteria
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Bacteria
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteria
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteria
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTCAGGCTAGAGTGTCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGG Bacteria
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Bacteria
## Phylum
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidetes
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Firmicutes
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroidetes
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidetes
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTCAGGCTAGAGTGTCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGG Firmicutes
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Firmicutes
## Class
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidia
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Clostridia
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroidia
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidia
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTCAGGCTAGAGTGTCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGG Clostridia
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Negativicutes
## Order
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidales
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Clostridiales
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroidales
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Bacteroidales
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTCAGGCTAGAGTGTCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGG Clostridiales
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Selenomonadales
## Family
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Prevotellaceae
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Ruminococcaceae
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroidaceae
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Prevotellaceae
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTCAGGCTAGAGTGTCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGG Lachnospiraceae
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Veillonellaceae
## Genus
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Prevotella
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT Faecalibacterium
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT Bacteroides
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT Prevotella
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTCAGGCTAGAGTGTCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGG <NA>
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG Dialister
## Species
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGACGCTCAACGTCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT copri
## ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT prausnitzii
## CCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGT <NA>
## CCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT <NA>
## GCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTCAGGCTAGAGTGTCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGG <NA>
## GCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGCTTCTTAAGTCCATCTTAAAAGTGCGGGGCTTAACCCCGTGATGGGATGGAAACTGAGAGGCTGGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCGGTGGCGAAGGCGACTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCGTGGGG <NA>write.table(sigtab_dds.dds.d7.broad, file="./results/deseq_d7_broad_Shedding.txt", sep = "\t") # Change filename to save results to appropriate file
# Quick check of factor levels
mcols(res.dds.d7.broad, use.names = TRUE)## DataFrame with 6 rows and 2 columns
## type
## <character>
## baseMean intermediate
## log2FoldChange results
## lfcSE results
## stat results
## pvalue results
## padj results
## description
## <character>
## baseMean mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): Shedding Shedding vs No.shedding
## lfcSE standard error: Shedding Shedding vs No.shedding
## stat Wald statistic: Shedding Shedding vs No.shedding
## pvalue Wald test p-value: Shedding Shedding vs No.shedding
## padj BH adjusted p-values# Prepare to join results data.table and taxonomy table
resdt.dds.d7.broad = data.table(as(results(dds.d7.broad, cooksCutoff = FALSE), "data.frame"),
keep.rownames = TRUE)
setnames(resdt.dds.d7.broad, "rn", "OTU")
taxdt.dds.d7.com = data.table(data.frame(as(tax_table(ps1.d7.broad), "matrix")), keep.rownames = TRUE)
setnames(taxdt.dds.d7.com, "rn", "OTU")
# Join results data.table and taxonomy table
setkeyv(taxdt.dds.d7.com, "OTU")
setkeyv(resdt.dds.d7.broad, "OTU")
resdt.dds.d7.broad <- taxdt.dds.d7.com[resdt.dds.d7.broad]
resdt.dds.d7.broad## OTU
## 1: ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 2: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
## 3: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
## 4: ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 5: ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
## ---
## 1586: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
## Kingdom Phylum Class Order
## 1: Bacteria Firmicutes Clostridia Clostridiales
## 2: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 3: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 4: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 5: Bacteria Firmicutes Clostridia Clostridiales
## ---
## 1586: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1587: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1588: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1589: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1590: Archaea Euryarchaeota Methanobacteria Methanobacteriales
## Family Genus Species baseMean
## 1: Ruminococcaceae NA NA 0.0000000
## 2: Fusobacteriaceae Fusobacterium nucleatum 0.0000000
## 3: Fusobacteriaceae Fusobacterium NA 0.0000000
## 4: Rikenellaceae NA NA 0.0000000
## 5: Eubacteriaceae Eubacterium NA 0.0000000
## ---
## 1586: Bacteroidaceae Bacteroides stercoris 0.0000000
## 1587: Bacteroidaceae Bacteroides NA 0.0000000
## 1588: Prevotellaceae Prevotella NA 0.0000000
## 1589: Prevotellaceae Prevotella bivia 0.0000000
## 1590: Methanobacteriaceae Methanobrevibacter NA 0.1071357
## log2FoldChange lfcSE stat pvalue padj
## 1: NA NA NA NA NA
## 2: NA NA NA NA NA
## 3: NA NA NA NA NA
## 4: NA NA NA NA NA
## 5: 0.0000000 0.000000 0.0000000 1.0000000 NA
## ---
## 1586: NA NA NA NA NA
## 1587: NA NA NA NA NA
## 1588: NA NA NA NA NA
## 1589: NA NA NA NA NA
## 1590: 0.9887598 3.145938 0.3142973 0.7532952 NAresdt.dds.d7.broad[, Significant := padj < alpha]
resdt.dds.d7.broad[!is.na(Significant)]## OTU
## 1: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 2: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAGACAAGTTGGAAGTGAAATCTATGGGCTCAACCCATAAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 3: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAGAACAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 4: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCAATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 5: ACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGCGATCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGATTGTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## ---
## 169: GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGAAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT
## 170: GCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGTAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGT
## 171: GCTAGCGTTATCCGGAATTACTGGGCGTAAAGGGTGCGTAGGTGGTTTCTTAAGTCAGAGGTGAAAGGCTACGGCTCAACCGTAGTAAGCCTTTGAAACTGGGAAACTTGAGTGCAGGAGAGGAGAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTTGCGAAGGCGGCTCTCTGGACTGTAACTGACACTGAGGCACGAAAGCGTGGGG
## 172: GCTAGCGTTATCCGGATTTACTGGGCGTAAAGGGTGCGTAGGCGGTCTTTCAAGTCAGGAGTGAAAGGCTACGGCTCAACCGTAGTAAGCTCTTGAAACTGGGAGACTTGAGTGCAGGAGAGGAGAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTTGCGAAGGCGGCTCTCTGGACTGTAACTGACGCTGAGGCACGAAAGCGTGGGG
## 173: GCTAGCGTTATCCGGATTTACTGGGCGTAAAGGGTGCGTAGGCGGTCTTTTAAGTCAGGAGTGAAAGGCTACGGCTCAACCGTAGTAAGCTCTTGAAACTGGAGGACTTGAGTGCAGGAGAGGAGAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTAGCGAAGGCGGCTCTCTGGACTGTAACTGACGCTGAGGCACGAAAGCGTGGGG
## Kingdom Phylum Class Order Family
## 1: Bacteria Firmicutes Clostridia Clostridiales Ruminococcaceae
## 2: Bacteria Firmicutes Clostridia Clostridiales Ruminococcaceae
## 3: Bacteria Firmicutes Clostridia Clostridiales Ruminococcaceae
## 4: Bacteria Firmicutes Clostridia Clostridiales Ruminococcaceae
## 5: Bacteria Firmicutes Clostridia Clostridiales Ruminococcaceae
## ---
## 169: Bacteria Firmicutes Bacilli Lactobacillales Lactobacillaceae
## 170: Bacteria Firmicutes Bacilli Lactobacillales Lactobacillaceae
## 171: Bacteria Firmicutes Clostridia Clostridiales Peptostreptococcaceae
## 172: Bacteria Firmicutes Clostridia Clostridiales Peptostreptococcaceae
## 173: Bacteria Firmicutes Clostridia Clostridiales Peptostreptococcaceae
## Genus Species baseMean log2FoldChange lfcSE
## 1: Faecalibacterium prausnitzii 166.405736 7.6272967 2.994864
## 2: Faecalibacterium prausnitzii 126.060421 4.1654154 2.758615
## 3: Faecalibacterium prausnitzii 4.048384 -5.4187547 3.112009
## 4: Faecalibacterium NA 3.464053 5.4671201 3.060913
## 5: Faecalibacterium prausnitzii 8.776203 3.5361118 3.004212
## ---
## 169: Lactobacillus NA 5.138507 21.0727267 3.058004
## 170: Lactobacillus NA 6.321005 21.3597980 3.056868
## 171: Romboutsia NA 74.444842 0.3313355 1.713318
## 172: Clostridium_XI difficile 5.001132 -20.8649778 3.110211
## 173: Intestinibacter bartlettii 36.437630 -0.5115360 1.690242
## stat pvalue padj Significant
## 1: 2.5467919 1.087182e-02 2.748332e-02 TRUE
## 2: 1.5099661 1.310521e-01 2.024286e-01 FALSE
## 3: -1.7412400 8.164151e-02 1.331695e-01 FALSE
## 4: 1.7861075 7.408186e-02 1.281616e-01 FALSE
## 5: 1.1770513 2.391750e-01 3.477082e-01 FALSE
## ---
## 169: 6.8910065 5.539901e-12 1.996673e-11 TRUE
## 170: 6.9874783 2.798709e-12 1.075948e-11 TRUE
## 171: 0.1933882 8.466550e-01 9.270336e-01 FALSE
## 172: -6.7085406 1.965805e-11 5.668070e-11 TRUE
## 173: -0.3026407 7.621637e-01 8.561969e-01 FALSEresdt.dds.d7.broad## OTU
## 1: ACAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGCGCAGGCGGGCCGGCAAGTTGGAAGTGAAATCTATGGGCTTAACCCATAAACTGCTTTCAAAACTGCTGGTCTTGAGTGATGGAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCCTACTGGGCACCAACTGACGCTGAGGCTCGAAAGTGTGGGT
## 2: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATATAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGT
## 3: ACAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGCATGACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTAAAGCGCGAAAGCGTGGGT
## 4: ACAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCTGTTTTTTAAGTTAGAGGTGAAAGCTCGACGCTCAACGTCGAAATTGCCTCTGATACTGAGAGACTAGAGTGTAGTTGCGGAAGGCGGAATGTGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 5: ACAAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGCGTAGGCGGTCTATTAAGTCTGATGTGAAAGGTACCGGCTCAACCGGTGAAGTGCATTGGAAACTGGTAGACTTGAGTATTGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACAAATACTGACGCTGAGGTGCGAAAGCGTGGGG
## ---
## 1586: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1587: TCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGGTTGTTAAGTCAGTTGTGGAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGCGACCTTGAGTGCAACAGAGGTAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTACTGGATTGTAACTGACGCTGATGCTCGAAAGTGTGGGT
## 1588: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGGAGATTAAGCGTGTTGTGAAATGTAGATGCTCAACATCTGCACTGCAGCGCGAACTGGTTTCCTTGAGTACGCACAAAGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGAGCGCAACTGACGCTGAAGCTCGAAAGTGCGGGT
## 1589: TCGGGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCCGTTTGGTAAGCGTGTTGTGAAATGTAGGAGCTCAACTTCTAGATTGCAGCGCGAACTGTCAGACTTGAGTGCGCACAACGTAGGCGGAATTCATGGTGTAGCGGTGAAATGCTTAGATATCATGAAGAACTCCGATTGCGAAGGCAGCTTACGGGAGCGCAACTGACGCTGAAGCTCGAAGGTGCGGGT
## 1590: TCTAGTGGTAGCAGTTTTTATTGGGCCTAAAGCGTCCGTAGCCGGTTTAATAAGTCTCTGGTGAAATCCTGCAGCTTAACTGTGGGAATTGCTGGAGATACTATTAGACTTGAGATCGGGAGAGGTTAGAGGTACTCCCAGGGTAGAGGTGAAATTCTGTAATCCTGGGAGGACCGCCTGTTGCGAAGGCGTCTGACTGGAACGATTCTGACGGTGAGGGACGAAAGCTAGGGG
## Kingdom Phylum Class Order
## 1: Bacteria Firmicutes Clostridia Clostridiales
## 2: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 3: Bacteria Fusobacteria Fusobacteriia Fusobacteriales
## 4: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 5: Bacteria Firmicutes Clostridia Clostridiales
## ---
## 1586: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1587: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1588: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1589: Bacteria Bacteroidetes Bacteroidia Bacteroidales
## 1590: Archaea Euryarchaeota Methanobacteria Methanobacteriales
## Family Genus Species baseMean
## 1: Ruminococcaceae NA NA 0.0000000
## 2: Fusobacteriaceae Fusobacterium nucleatum 0.0000000
## 3: Fusobacteriaceae Fusobacterium NA 0.0000000
## 4: Rikenellaceae NA NA 0.0000000
## 5: Eubacteriaceae Eubacterium NA 0.0000000
## ---
## 1586: Bacteroidaceae Bacteroides stercoris 0.0000000
## 1587: Bacteroidaceae Bacteroides NA 0.0000000
## 1588: Prevotellaceae Prevotella NA 0.0000000
## 1589: Prevotellaceae Prevotella bivia 0.0000000
## 1590: Methanobacteriaceae Methanobrevibacter NA 0.1071357
## log2FoldChange lfcSE stat pvalue padj Significant
## 1: NA NA NA NA NA NA
## 2: NA NA NA NA NA NA
## 3: NA NA NA NA NA NA
## 4: NA NA NA NA NA NA
## 5: 0.0000000 0.000000 0.0000000 1.0000000 NA NA
## ---
## 1586: NA NA NA NA NA NA
## 1587: NA NA NA NA NA NA
## 1588: NA NA NA NA NA NA
## 1589: NA NA NA NA NA NA
## 1590: 0.9887598 3.145938 0.3142973 0.7532952 NA NAvolcano.d7.broad.shed = ggplot(
data = resdt.dds.d7.broad[!is.na(Significant)][(pvalue < 1)],
mapping = aes(x = log2FoldChange,
y = -log10(pvalue),
color = Phylum,
label = OTU, label1 = Genus)) +
theme_bw() +
geom_point() +
geom_point(data = resdt.dds.d7.broad[(Significant)], size = 7, alpha = 0.7) +
# geom_text(data = resdt[(Significant)], mapping = aes(label = paste("Genus:", Genus)), color = "black", size = 3) +
theme(axis.text.x = element_text(angle = -90, hjust = 0, vjust=0.5)) +
geom_hline(yintercept = -log10(alpha)) +
ggtitle("DESeq2 Negative Binomial Test Volcano Plot\nDay 7 Broad Spectrum Antibiotics ~ Shedding") +
theme(axis.title = element_text(size=12)) +
theme(axis.text = element_text(size=12)) +
theme(legend.text = element_text(size=12)) +
geom_vline(xintercept = 0, lty = 2)
volcano.d7.broad.shed
summary(res.dds.d7.broad)##
## out of 365 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up) : 77, 21%
## LFC < 0 (down) : 9, 2.5%
## outliers [1] : 0, 0%
## low counts [2] : 316, 87%
## (mean count < 3)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?resultsmcols(res.dds.d7.broad, use.names = TRUE)## DataFrame with 6 rows and 2 columns
## type
## <character>
## baseMean intermediate
## log2FoldChange results
## lfcSE results
## stat results
## pvalue results
## padj results
## description
## <character>
## baseMean mean of normalized counts for all samples
## log2FoldChange log2 fold change (MLE): Shedding Shedding vs No.shedding
## lfcSE standard error: Shedding Shedding vs No.shedding
## stat Wald statistic: Shedding Shedding vs No.shedding
## pvalue Wald test p-value: Shedding Shedding vs No.shedding
## padj BH adjusted p-valuesggplotly(volcano.d7.broad.shed)grid.arrange(volcano.d.9.narrow.shed, volcano.d0.narrow.shed, volcano.d7.narrow.shed, volcano.d.9.broad.shed, volcano.d0.broad.shed, volcano.d7.broad.shed, ncol = 3, nrow = 3)
BOOST: Day 7 Narrow vs. Broad
sample_data(ps1)$day
sample_data(ps1)$d7_rota_boost_updated
sample_data(ps1)$randomization_arm
ps1.d7.boost_narrow_v_broad <- ps1 %>%
subset_samples(
day == "7" &
d7_rota_boost_updated == "Yes" &
randomization_arm != "No antibiotics"
)
sample_data(ps1.d7.boost_narrow_v_broad)$day
sample_data(ps1.d7.boost_narrow_v_broad)$d7_rota_boost_updated
sample_data(ps1.d7.boost_narrow_v_broad)$randomization_arm
# Differential Abundance Testing
ds.d7.boost_narrow_v_broad <- phyloseq_to_deseq2(ps1.d7.boost_narrow_v_broad, ~randomization_arm)
geoMeans.ds.d7.boost_narrow_v_broad <- apply(counts(ds.d7.boost_narrow_v_broad), 1, gm_mean)
ds.d7.boost_narrow_v_broad <- estimateSizeFactors(ds.d7.boost_narrow_v_broad, geoMeans = geoMeans.ds.d7.boost_narrow_v_broad)
dds.d7.boost_narrow_v_broad <- DESeq(ds.d7.boost_narrow_v_broad, test="Wald", fitType="local", betaPrior = FALSE)
alpha = 0.05
# Tabulate and write results
res.dds.d7.boost_narrow_v_broad = results(dds.d7.boost_narrow_v_broad, cooksCutoff = FALSE)
sigtab_dds.dds.d7.boost_narrow_v_broad = res.dds.d7.boost_narrow_v_broad[which(res.dds.d7.boost_narrow_v_broad$padj < alpha), ]
sigtab_dds.dds.d7.boost_narrow_v_broad = cbind(as(sigtab_dds.dds.d7.boost_narrow_v_broad, "data.frame"), as(tax_table(ps1.d7.boost_narrow_v_broad)[rownames(sigtab_dds.dds.d7.boost_narrow_v_broad), ], "matrix"))
summary(res.dds.d7.boost_narrow_v_broad)
head(sigtab_dds.dds.d7.boost_narrow_v_broad)
write.table(sigtab_dds.dds.d7.boost_narrow_v_broad, file="./results/deseq_d7_boosted_samples.txt", sep = "\t") # Change filename to save results to appropriate file
# Quick check of factor levels
mcols(res.dds.d7.boost_narrow_v_broad, use.names = TRUE)
# Prepare to join results data.table and taxonomy table
resdt.dds.d7.boost_narrow_v_broad = data.table(as(results(dds.d7.boost_narrow_v_broad, cooksCutoff = FALSE), "data.frame"),
keep.rownames = TRUE)
setnames(resdt.dds.d7.boost_narrow_v_broad, "rn", "OTU")
taxdt.dds.d0.com = data.table(data.frame(as(tax_table(ps1.d7.boost_narrow_v_broad), "matrix")), keep.rownames = TRUE)
setnames(taxdt.dds.d0.com, "rn", "OTU")
# Join results data.table and taxonomy table
setkeyv(taxdt.dds.d0.com, "OTU")
setkeyv(resdt.dds.d7.boost_narrow_v_broad, "OTU")
resdt.dds.d7.boost_narrow_v_broad <- taxdt.dds.d0.com[resdt.dds.d7.boost_narrow_v_broad]
resdt.dds.d7.boost_narrow_v_broad
resdt.dds.d7.boost_narrow_v_broad[, Significant := padj < alpha]
resdt.dds.d7.boost_narrow_v_broad[!is.na(Significant)]
resdt.dds.d7.boost_narrow_v_broad
volcano.d7.boost_narrow_v_broad_v_treatment = ggplot(
data = resdt.dds.d7.boost_narrow_v_broad[!is.na(Significant)][(pvalue < 1)],
mapping = aes(x = log2FoldChange,
y = -log10(pvalue),
color = Phylum,
label = OTU, label1 = Genus)) +
theme_bw() +
geom_point() +
geom_point(data = resdt.dds.d7.boost_narrow_v_broad[(Significant)], size = 7, alpha = 0.7) +
# geom_text(data = resdt[(Significant)], mapping = aes(label = paste("Genus:", Genus)), color = "black", size = 3) +
theme(axis.text.x = element_text(angle = -90, hjust = 0, vjust=0.5)) +
geom_hline(yintercept = -log10(alpha)) +
ggtitle("DESeq2 Negative Binomial Test Volcano Plot\nDay 7 Boosted ~ Narrow Vs. Broad") +
theme(axis.title = element_text(size=12)) +
theme(axis.text = element_text(size=12)) +
theme(legend.text = element_text(size=12)) +
geom_vline(xintercept = 0, lty = 2)
volcano.d7.boost_narrow_v_broad_v_treatment
summary(res.dds.d7.boost_narrow_v_broad)
mcols(res.dds.d7.boost_narrow_v_broad, use.names = TRUE)
ggplotly(volcano.d7.boost_narrow_v_broad_v_treatment)